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Conformational dynamics play a crucial role in protein functions. A molecular-level understanding of the conformational transition dynamics of proteins is fundamental for studying protein functions. Here, we report a study of real-time conformational dynamic interaction between calcium-activated calmodulin (CaM) and C28W peptide using single-molecule fluorescence resonance energy transfer (FRET) spectroscopy and imaging. Plasma membrane Ca-ATPase protein interacts with CaM by its peptide segment that contains 28 amino acids (C28W). The interaction between CaM and the Ca-ATPase is essential for cell signaling. However, details about its dynamic interaction are still not clear. In our current study, we used Cyanine3 labeled CaM (N-domain) and Dylight 649 labeled C28W peptide (N-domain) to study the conformational dynamics during their interaction. In this study, the FRET can be measured when the CaM-C28W complex is formed and only be observed when such a complex is formed. By using single-molecule FRET efficiency trajectory and unique statistical approaches, we were able to observe multiple binding steps with detailed dynamic features of loosely bound and tightly bound state fluctuations. The C-domain of CaM tends to bind with C28W first with a higher affinity, followed by the binding of the CaM N-domain. Due to the comparatively high flexibility and low affinity of the N-domain and the presence of multiple anchor hydrophobic residues on the peptide, the N-domain binding may switch between selective and non-selective binding states, while the C-domain remains strongly bound with C28W. The results provide a mechanistic understanding of the CaM signaling interaction and activation of the Ca-ATPase through multiple-state binding to the C28W. The new single-molecule spectroscopic analyses demonstrated in this work can be applied for broad studies of protein functional conformation fluctuation and protein-protein interaction dynamics.

Oscillatory processes are essential for normal functioning and survival of biological systems, and reactive oxygen species have a prominent role in many of them. A mechanism representing the dynamics of these species in the rhizosphere is analyzed using stoichiometric network analysis with the aim to determine its capabilities to simulate various dynamical states, including oscillations. A detailed analysis has shown that unstable steady states result from four destabilizing feedback cycles, among which the cycle involving hydroquinone, an electron acceptor, and its semi-reduced form is the dominant one responsible for the existence of saddle-node and Andronov–Hopf bifurcations. This requires a higher steady-state concentration for the reduced electron acceptor compared to that of the remaining species, where the level of oxygen steady-state concentration determines whether the Andronov–Hopf or saddle-node bifurcation will occur.

By using coarse-grained molecular dynamics simulations, we have investigated the structure and dynamics of supercooled single-chain cross-linked nanoparticle (SCNP) melts having a range of cross-linking degrees ϕ. We find a nearly linear increase in glass-transition temperature (Tg) with increasing ϕ. Correspondingly, we have also experimentally synthesized a series of polystyrene-based SCNPs and have found that the measured Tg estimated from differential scanning calorimetry is qualitatively consistent with the trend predicted by our simulation estimates. Experimentally, an increase in Tg as large as ΔTg = 61 K for ϕ = 0.36 is found compared with their linear chain counterparts, indicating that the changes in dynamics with cross-links are quite appreciable. We attribute the increase in Tg to the enlarged effective hard-core volume and the corresponding reduction in the free volume of the polymer segments. Topological constraints evidently frustrate the local packing. In addition, the introduction of intra-molecular cross-linking bonds slows down the structural relaxation and simultaneously enhances the local coupling motion on the length scales within SCNPs. Consequently, a more pronounced dynamical heterogeneity (DH) is observed for larger ϕ, as quantified by measuring the dynamical correlation length through the four-point susceptibility parameter, χ4. The increase in DH is directly related to the enhanced local cooperative motion derived from intra-molecular cross-linking bonds and structural heterogeneity derived from the cross-linking process. These results shed new light on the influence of intra-molecular topological constraints on the segmental dynamics of polymer melts.

Intermolecular interactions between cholesterol and lipids in cell membranes, which play critical roles in cellular processes such as the formation of nano-domains, depend on the molecular structure of the lipids. The diffusion and the spatial arrangement of cholesterol within the lipid membranes also change with the type of lipids. For example, the flip-flop, an important transport mechanism for cholesterol in the membranes, can be facilitated significantly by the presence of unsaturated lipids. However, how the structure of lipids affects the spatial arrangement and the dynamics of cholesterol remains elusive at a molecular level. In this study, we investigate the effects of lipid–cholesterol interactions on the spatial arrangement and the dynamics of cholesterol. We perform molecular dynamics simulations for the binary component membranes of lipids and cholesterol. We employ seven different kinds of lipids by changing either the degree of a saturation level or the length of lipid tails. We find from our simulations that the rate of cholesterol flip-flop is enhanced as the lipids are either less saturated or shorter, which is consistent with previous studies. Interestingly, when the lipid tails are fully saturated and sufficiently long, the center in between two leaflets becomes metastable for cholesterol to stay at. Because the cholesterol at the membrane center diffuses faster than that within leaflets, regardless of the lipid type, such an emergence of the metastable state (in terms of the cholesterol position) complicates the cholesterol diffusion significantly.

Configuration dynamics of flexible polymer chains is of ubiquitous importance in many biological processes. Here, we investigate a polymer chain immersed in a bath of size-changed active particles in two dimensional space using Langevin dynamics simulations. Particular attention is paid to how the radius of gyration Rg of the polymer chain depends on the size σc of active crowders. We find that Rg shows nontrivial non-monotonic dependence on σc: The chain first swells upon increasing σc, reaching a fully expanded state with maximum Rg, and then, Rg decreases until the chain collapses to a compact coil state if the crowder is large enough. Interestingly, the chain may oscillate between a collapse state and a stretched state at moderate crowder size. Analysis shows that it is the competition between two effects of active particles, one stretching the chain from inside due to persistence motion and the other compressing the chain from outside, that leads to the non-monotonic dependence. Besides, the diffusion of the polymer chain also shows nontrivial non-monotonic dependence on σc. Our results demonstrate the important interplay between particle activity and size associated with polymer configurations in active crowding environments.

The external voltage-driven polymer translocation through a conical pore (with a large opening at the entry and a small tip at the exit) is studied by using the Langevin dynamics simulation in this paper. The entire translocation process is divided into an approaching stage and a threading stage. First, the approaching stage starts from the polymer entering the large opening and ends up at a terminal monomer reaching the pore tip. In this stage, the polymer will undergo the conformation adjustment to fit the narrowed cross-sectional area of the pore, leading to three approaching modes: the non-stuck mode with a terminal monomer arriving at the pore tip smoothly, the weak-stuck mode for the polymer stuck inside the pore for a short duration with minor conformational adjustments, and the strong-stuck mode with major conformational changes and a long duration. The approaching times (the duration of the approaching stage) of the three approaching modes show different behavior as a function of the pore apex angle. Second, the threading stage describes that the polymer threads through the pore tip with a linear fashion. In this stage, an increase in the apex angle causes the reduction of the threading time (the duration of the threading stage) due to the increase in the driving force with the apex angle at the tip. Moreover, we also find that with the increase in the apex angle or the polymer length, the polymer threading dynamics will change from the quasi-equilibrium state to the non-equilibrium state.

Dynamic coupling with water contributes to regulating the functional dynamics of a biomolecule. We discuss protein-water dynamics, with emphasis on water that is partially confined, and the role of protein-confined water dynamics in allosteric regulation. These properties are illustrated with two systems, a homodimeric hemoglobin from Scapharca inaequivalvis (HbI) and an A2A adenosine receptor (A2AAR). For HbI, water-protein interactions, long known to contribute to the thermodynamics of cooperativity, are seen to influence the dynamics of the protein not only around the protein-water interface but also into the core of each globule, where dynamic and entropic changes upon ligand binding are coupled to protein-water contact dynamics. Similarly, hydration waters trapped deep inside the core region of A2AAR enable the formation of an allosteric network made of water-mediated inter-residue contacts. Extending from the ligand binding pocket to the G-protein binding site, this allosteric network plays key roles in regulating the activity of the receptor.

One of the many ways cells transmit information within their volume is through steady spatial gradients of different proteins. However, the mechanism through which proteins without any sources or sinks form such single-cell gradients is not yet fully understood. One of the models for such gradient formation, based on differential diffusion, is limited to proteins with large ratios of their diffusion constants or to specific protein-large molecule interactions. We introduce a novel mechanism for gradient formation via the coupling of the proteins within a single cell with a molecule, that we call a "pronogen", whose action is similar to that of morphogens in multi-cell assemblies, the pronogen is produced with a fixed flux at one side of the cell. This coupling results in an effectively non-linear diffusion degradation model for the pronogen dynamics within the cell, which leads to a steady-state gradient of the protein concentration. We use a stability analysis to show that these gradients are linearly stable with respect to perturbations., Comment: To appear in J. Chem. Phys

In this paper, the second in a series devoted to molecular modeling of protein aggregation, a mesoscale model of proteins together with extensive discontinuous molecular dynamics simulation is used to study the phenomenon in a confined medium. The medium, as a model of a crowded cellular environment, is represented by a spherical cavity, as well as cylindrical tubes with two aspect ratios. The aggregation process leads to the formation of β sheets and eventually fibrils, whose deposition on biological tissues is believed to be a major factor contributing to many neuro-degenerative diseases, such as Alzheimer's, Parkinson's, and amyotrophic lateral sclerosis diseases. Several important properties of the aggregation process, including dynamic evolution of the total number of the aggregates, the mean aggregate size, and the number of peptides that contribute to the formation of the β sheets, have been computed. We show, similar to the unconfined media studied in Paper I [S. Zheng et al., J. Chem. Phys. 145, 134306 (2016)], that the computed properties follow dynamic scaling, characterized by power laws. The existence of such dynamic scaling in unconfined media was recently confirmed by experiments. The exponents that characterize the power-law dependence on time of the properties of the aggregation process in spherical cavities are shown to agree with those in unbounded fluids at the same protein density, while the exponents for aggregation in the cylindrical tubes exhibit sensitivity to the geometry of the system. The effects of the number of amino acids in the protein, as well as the size of the confined media, have also been studied. Similarities and differences between aggregation in confined and unconfined media are described, including the possibility of no fibril formation, if confinement is severe.

We investigate the phase separation behavior of binary mixtures in two-dimensional periodic and confined domains using dissipative particle dynamics. Two canonical problems of fluid mechanics are considered for the confined domains: square cavity with no-slip walls and lid-driven cavity with one driven wall. The dynamics is studied for both weakly and strongly separating mixtures and different area fractions. The phase separation process is analyzed using the structure factor and the total interface length. The dynamics of phase separation in the square cavity and lid-driven cavity are observed to be significantly slower when compared to the dynamics in the periodic domain. The presence of the no-slip walls and the inertial effects significantly influences the separation dynamics. Finally, we show that the growth exponent for the strongly separating case is invariant to changes in the inter-species repulsion parameter.

Using the Anderson-Holstein model, we investigate charge transfer dynamics between a molecule and a metal surface for two extreme cases. (i) With a large barrier, we show that the dynamics follow a single exponential decay as expected; (ii) without any barrier, we show that the dynamics are more complicated. On the one hand, if the metal-molecule coupling is small, single exponential dynamics persist. On the other hand, when the coupling between the metal and the molecule is large, the dynamics follow a biexponential decay. We analyze the dynamics using the Smoluchowski equation, develop a simple model, and explore the consequences of biexponential dynamics for a hypothetical cyclic voltammetry experiment.

We present a thorough analysis of the dynamic behaviour of hybrid atomistic/coarse-grained (CG) models of polymer melts. While structural properties are well preserved in a dual-resolved model, we show how the dynamic of the chains can be influenced by the simultaneous presence of atoms and beads. We show that although the polymer chains are long enough to exhibit reptation, the corresponding CG model is unable to capture the expected subdiffusive regimes and seems to still follow the Rouse dynamics. The introduction of atoms in the chain restores the correct dynamic regime, and the dynamics of hybrid systems becomes comparable to that of the atomistic dynamics as the atoms/beads ratio is increased.

We examine the population dynamics of naturally folded globular polymers, with a super-hydrophobic "core" inserted at a prescribed point in the polymer chain, unfolding under an application of external force, as in AFM force-clamp spectroscopy. This acts as a crude model for a large class of folded biomolecules with hydrophobic or hydrogen-bonded cores. We find that the introduction of super-hydrophobic units leads to a stochastic variation in the unfolding rate, even when the positions of the added monomers are fixed. This leads to the average non-exponential population dynamics, which is consistent with a variety of experimental data and does not require any intrinsic quenched disorder that was traditionally thought to be at the origin of non-exponential relaxation laws.

The self-assembly of molecular building blocks into linear filaments is a common form of self-organization in nature and underlies the formation of supra-molecular polymers in a variety of contexts, including in both functional and aberrant biology. To date, attention has focused mainly on homomolecular assembly phenomena; however, it has recently become apparent that heteromolecular assemblies can be common, and, for instance, pathological protein filaments such as amyloid aggregates form in vivo in environments supporting copolymerization. Here, we present a general kinetic scheme for heteromolecular filament formation and derive closed-form analytical expressions that describe the dynamics of such systems. Our results reveal the existence of a demixing transition time controlled by the relative rates of depletion of the different aggregating species, after which predominantly homomolecular polymers are formed even when the initial solution is heteromolecular. Furthermore, these results may be applied to the analysis of experimental kinetic data on the aggregation of mixtures of proteins, to determine which fundamental reaction steps occur between unlike proteins, and to provide accurate estimates of their rate constants.

The ability to separate proteins is desirable for many fields of study, and nanoporous membranes may offer a method for rapid protein filtration at high throughput volume, provided there is an understanding of the protein dynamics involved. In this work, we use Brownian dynamics simulations to study the motion of coarse-grained proteins insulin and ubiquitin in an electrically biased membrane. In our model, the protein is subjected to various biases applied to the silicon membrane equipped with a nanopore of different radii. The time each protein takes to find a cylindrical nanopore embedded in a thin silicon membrane, attempt to translocate it (waiting time), and successfully translocate it in a single attempt (translocation time) is calculated. We observe insulin finding the nanopore and translocating it faster than the electrically neutral ubiquitin due to insulin’s slightly smaller size and net negative charge. While ubiquitin’s dynamics is also affected by the size of the pore, surprisingly, its translocation process is also noticeably changed by the membrane bias. By investigating the protein’s multipole moments, we demonstrate that this behavior is largely due to the protein’s dipole and quadrupole interactions with the membrane potential.The ability to separate proteins is desirable for many fields of study, and nanoporous membranes may offer a method for rapid protein filtration at high throughput volume, provided there is an understanding of the protein dynamics involved. In this work, we use Brownian dynamics simulations to study the motion of coarse-grained proteins insulin and ubiquitin in an electrically biased membrane. In our model, the protein is subjected to various biases applied to the silicon membrane equipped with a nanopore of different radii. The time each protein takes to find a cylindrical nanopore embedded in a thin silicon membrane, attempt to translocate it (waiting time), and successfully translocate it in a single attempt (translocation time) is calculated. We observe insulin finding the nanopore and translocating it faster than the electrically neutral ubiquitin due to insulin’s slightly smaller size and net negative charge. While ubiquitin’s dynamics is also affected by the size of the pore, surprisingly, its tran...

We study theoretically the physical properties of Rouse polymers when a subset of monomers along the backbone is subjected to an additional driving force of exponentially correlated fluctuating noise. In other words, the polymers are made up of two kinds of particle, one of which has an additional coupling to an active bath that subjects those particles to extra forces. We analyze properties of these active polymers, such as the end to end distance and the local structure induced by active kicks. We then proceed to quantify how the dynamics of such polymers depend on the proportion of monomers which are being actively driven, and show how the dynamics transitions from the normal Rouse like behavior to substantially faster dynamics. Finally we analyze some of the non-equilibrium properties induced in these systems, such as the irreversibility.

Using extrinsic probes to study a host system relies on the probes’ ability to accurately report the host properties under study. Probes have long been used to characterize dynamic heterogeneity, the phenomenon in which a liquid near its glass transition exhibits distinct dynamics as a function of time and position, with molecules within nanometers of each other exhibiting dynamics that may vary by orders of magnitude. The spatial and temporal characteristics of dynamic heterogeneity demand the selection of probes using stringent criteria on their size and dynamics. In this report, we study the dynamic heterogeneity of the prototypical molecular glass former o-terphenyl by investigating single molecule rotation of two perylene dicarboximide probe molecules that differ in size and comparing this to results obtained previously with the probe BODIPY268. It is found that a probe’s ability to accurately report dynamic heterogeneity in o-terphenyl depends on whether the reported distribution of dynamics overlaps with the intrinsic dynamics of the host, which is naturally related to the width of the intrinsic dynamics and the magnitude of dynamical shift in probe dynamics relative to the host. We show that a probe that rotates ≈15 times more slowly than the intrinsic dynamics of the host o-terphenyl senses the slowest ≈5% of the full dynamic heterogeneity whereas one that rotates ≈65 times more slowly than the host fails to report dynamic heterogeneity of the host.

Molecular excitation with incoherent light is examined using realistic turn-on time scales, and results are compared to those obtained via commonly used sudden turn-on, or pulses. Two significant results are obtained. First, in contrast to prior studies involving sudden turn-on, realistic turn-on is shown to lead to stationary coherences for natural turn-on time scales. Second, the time to reach the final stationary mixed state, known to result from incoherent excitation, is shown to depend directly on the inverse of the molecular energy level spacings, in both sudden and realistic turn-on cases. The S0 → S2/S1 internal conversion process in pyrazine is used as an example throughout. Implications for studies of natural light harvesting systems are noted.

Causative to the neurodegenerative Huntington’s disease (HD), a mutational huntingtin (HTT) protein consists of an unusual expansion on the poly-glutamine (polyQ) region in the first exon (exon-1) domain. Despite its significance on HD progression, the structural role of the exon-1 with the polyQ region is still elusive. As HTT is an intrinsically disordered protein (IDP), a large ensemble of various conformations (instead of a mostly single native conformation) is required to characterize its structural properties and to infer biological functions, which is challenging even for the most state-of-the-art experimental techniques. For this reason, molecular dynamics (MD) simulations with enhanced sampling techniques are ideal to compliment experiment on collecting such a large ensemble of thermodynamically accessible structures. Here, we performed large-scale temperature replica-exchange MD (T-REMD) simulations on the exon-1 with an illustration on the necessity of using T-REMD instead of unbiased regular MD. By comparing T-REMD data and unbiased MD data, we discovered that (1) the dynamics of polyQ regions are extremely sluggish and glassy at the room temperature and the relaxation of the system cannot be achieved within a reasonable amount of time without utilizing an enhanced sampling method and (2) an ensemble of protein structures containing the surprising cis-peptide bonds in the proline-rich domain can be obtained at much elevated temperatures. Our results may provide valuable insights for future studies on the HTT as well as other IDPs using the T-REMD method.

This article presents an investigation of the interparticle interactions and dynamics of submicron silica colloids suspended in a bath of motile Escherichia coli bacteria. The colloidal microstructure and dynamics were probed by ultra-small-angle x-ray scattering and multi-speckles x-ray photon correlation spectroscopy, respectively. Both static and hydrodynamic interactions were obtained for different colloid volume fractions and bacteria concentrations as well as when the interparticle interaction potential was modified by the motility buffer. Results suggest that motile bacteria reduce the effective attractive interactions between passive colloids and enhance their dynamics at high colloid volume fractions. The enhanced dynamics under different static interparticle interactions can be rationalized in terms of an effective viscosity of the medium and unified by means of an empirical effective temperature of the system. While the influence of swimming bacteria on the colloid dynamics is significantly lower for small particles, the role of motility buffer on the static and dynamic interactions becomes more pronounced.This article presents an investigation of the interparticle interactions and dynamics of submicron silica colloids suspended in a bath of motile Escherichia coli bacteria. The colloidal microstructure and dynamics were probed by ultra-small-angle x-ray scattering and multi-speckles x-ray photon correlation spectroscopy, respectively. Both static and hydrodynamic interactions were obtained for different colloid volume fractions and bacteria concentrations as well as when the interparticle interaction potential was modified by the motility buffer. Results suggest that motile bacteria reduce the effective attractive interactions between passive colloids and enhance their dynamics at high colloid volume fractions. The enhanced dynamics under different static interparticle interactions can be rationalized in terms of an effective viscosity of the medium and unified by means of an empirical effective temperature of the system. While the influence of swimming bacteria on the colloid dynamics is significantly low...

Room temperature ionic liquids (RTILs) have been shown to exhibit spatial heterogeneity or structural heterogeneity in the sense that they form hydrophobic and ionic domains. Yet studies of the relationship between this structural heterogeneity and the ∼picosecond motion of the molecular constituents remain limited. In order to obtain insight into the time scales relevant to this structural heterogeneity, we perform molecular dynamics simulations of a series of RTILs. To investigate the relationship between the structures, i.e., the presence of hydrophobic and ionic domains, and the dynamics, we gradually increase the size of the hydrophobic part of the cation from ethylammonium nitrate (EAN), via propylammonium nitrate (PAN), to butylammonium nitrate (BAN). The two ends of the organic cation, namely, the charged Nhead–H group and the hydrophobic Ctail–H group, exhibit rotational dynamics on different time scales, evidencing dynamical heterogeneity. The dynamics of the Nhead–H group is slower because of t...

Relationship between segmental relaxation and normal-mode relaxation has been studied for molten poly(butylene oxide)s having various molecular weights by broadband dielectric spectroscopy over a wide temperature (T) range. We found that T dependence of the segmental relaxation time, τs, was weaker than the normal mode time, τn, at high T(>250 K ∼ Tg + 50 K), and the τn/τs ratio systematically decreased with increasing temperature. This high temperature complexity, whose mechanism has not been discussed in detail so far, was quantitatively explained by assuming the two step processes: local conformation change of polymers (elementary process) occurs first, and then the motion of a segment unit (second process) occurs. It was also found that the elementary process was strongly correlated with the experimentally observed β-relaxation.

The dynamics of fluid confined in a nano-channel with smooth walls have been studied through velocity autocorrelation function within the memory function approach by incorporating the atomic level interactions of fluid with the confining wall. Expressions for the second and fourth sum rules of velocity autocorrelation have been derived for nano-channel which involves fluid-fluid and fluid-wall interactions. These expressions, in addition, involve pair correlation function and density profiles. The numerical contributions of fluid-wall interaction to sum rules are found to play a very significant role, specifically at smaller channel width. Results obtained for velocity autocorrelation and self-diffusion coefficient of a fluid confined to different widths of the nanochannel have been compared with the computer simulation results. The comparison shows a good agreement except when the width of the channel is of the order of two atomic diameters, where it becomes difficult to estimate sum rules involving the triplet correlation’s contribution.

Polymer translocation through nanopore has potential technological applications for DNA sequencing, where one challenge problem is to slow down translocation speed. Inspired by experimental findings that kinked nanopores exhibit a large reduction in translocation velocity compared with their straight counterparts, we investigate the dynamics of polymer translocation through kinked nanopores in two dimensions under an applied external field. With increasing the tortuosity of an array of nanopores, our analytical results show that the translocation probability decreases. Langevin dynamics simulation results support this prediction and further indicate that with increasing the tortuosity, translocation time shows a slow increase followed by a rapid increase after a critical tortuosity. This behavior demonstrates that kinked nanopores can effectively reduce translocation speed. These results are interpreted by the roles of the tortuosity for decreasing the effective nanopore diameter, increasing effective nanopore length, and greatly increasing the DNA-pore friction.

DNA-binding proteins locate and bind their target sequences positioned on DNA in crowded environments, but the molecular crowding effect on this search process is not clear. Using analytical techniques and Langevin dynamics simulations in two dimensions (2D), we find that the essential physics for facilitated diffusion in 2D search and 3D search is the same. We observe that the average search times have minima at the same optimal nonspecific binding energy for the cases with and without the crowding particle. Moreover, the molecular crowding increases the search time by increasing the average search rounds and the one-dimensional (1D) sliding time of a round, but almost not changing the average 2D diffusion time of a round. In addition, the fraction of 1D sliding time out of the total search time increases with increasing the concentration of crowders. For 2D diffusion, the molecular crowding decreases the jumping length and narrows its distribution due to the cage effect from crowders. These results shed light on the role of facilitated diffusion in DNA targeting kinetics in living cells.

The reaction C2 + C6H2 → C8H + H was investigated for the first time. Reactant C2 (C6H2) was synthesized from 1% C3F6/He (5% C2H2/He) by pulsed high-voltage discharge. We measured the translational-energy distribution, the angular distribution, and the photoionization spectrum of product C8H in a crossed molecular-beam apparatus using synchrotron vacuum-ultraviolet ionization. This reaction released average translational energy of 8.5 kcal mol(-1) corresponding to a fraction of 0.37 in translation. C8H was identified as octatetranyl based on the maximal translational-energy release 23 ± 2 kcal mol(-1) and the ionization threshold 8.9 ± 0.2 eV. Kinematic constraints can qualitatively account for the nearly isotropic angular distribution. The quantum-chemical calculations indicate that the exothermic reactions C2 (X (1)Σg (+)/a (3)Πu) + HC6H → C8H + H can proceed without entrance and exit barriers, implying the importance in the cold interstellar medium. This work verifies that interstellar C8H can be formed through the C2 + C6H2 reaction.

In this article, we use cooling-rate dependent Tg measurements (CR-Tg) to indirectly probe the relaxation dynamics of supported polystyrene thin films of various molecular weights, all chosen to be above the entanglement molecular weight. We show that the dynamics in these films deviate from bulk dynamics below a temperature T(*) = Tg + 6 K = 380 K ± 1 K. We show that T(*) for films of all thicknesses and molecular weights is the same as the temperature at which the free surface dynamics deviate from the bulk dynamics. The apparent activation barrier of the glass transition in thin films decreases towards that of the free surface as the film thickness decreases. This provides strong evidence that thin film dynamics are facilitated by the enhanced mobility at the free surface. The observation of T(*) can help resolve some seemingly contradictory data by suggesting that studies performed at higher temperatures (TT(*)), or which probe shorter relaxation times (ττ(*) ∼ 1 s) would not observe properties that deviate from bulk values. We also demonstrate that the relaxation dynamics of supported entangled polystyrene films slow down slightly as the molecular weight of polystyrene increases. An eight nanometer film of Mw =2240 kg/mol polystyrene shows a Tg reduction of 27 K at a cooling rate of 1 K/min, while a film of the same thickness made of Mw =45.8 kg/mol polystyrene has a 36 K reduction of Tg compared to the bulk film at the same cooling rate. We hypothesize this is either due to the density of a dynamically "dead" layer near the substrate increasing with molecular weight, or partial anchoring of long chains, which could hinder segmental diffusion near the free surface.

Electron-nuclear relaxation dynamics are studied in Hg(n) (-) (11or= nor= 16,n = 18) using time-resolved photoelectron imaging. The excess electron in the anion uniquely occupies the p band and is excited intraband by 1.53 eV pump photons; the subsequent dynamics are monitored by photodetachment at 3.06 eV and measurement of the photoelectron images as a function of pump-probe delay. The initially excited state decays on a time scale of approximately 10 ps, and subsequent relaxation dynamics reveal a smooth evolution of the photoelectron spectra towards lower electron kinetic energy over 50-100 ps. Qualitatively, the relaxation process is captured by a simple kinetic model assuming a series of radiationless transitions within a dense manifold of electronic states. All the clusters studied show similar dynamics with the exception of Hg(11) (-) in which the initially prepared state does not decay as quickly as the others.

We report observations of photocontrolled oscillatory behavior in the 1,4-cyclohexanedione- bromate reaction (CHD—cyclohexanedione). Experiments in a batch reactor show that illumination may exhibit qualitatively different effects on the reaction dynamics, where illumination with a moderate intensity favors oscillations while strong illumination quenches spontaneous oscillations. A transition from light-quenched to light-induced oscillations during the course of the reaction has also been observed. Investigations in a continuous flow stirred tank reactor further illustrate that the influence of light in the 1,4-CHD-bromate reaction depends not only on the intensity of the illumination but also on the phase at which the illumination is switched on. Mechanistic investigations suggest that 1,4-benzoquinone, a final product in the 1,4-CHD-bromate reaction system, plays a significant role in the occurrence of photoinduced oscillations.

The influence of the bead-bead interaction on the rotational dynamics of macromolecules which are immersed into a solution has been investigated by starting from the microscopic theory of the macromolecular motion, i.e., from a Fokker-Planck equation for the phase-space distribution function. From this equation, we then derived an explicit expression for the configuration-space distribution function of a nonrigid molecule which is immobilized on a surface. This function contains all the information about the interaction among the beads as well as the effects from the surrounding solvent particles and from the surface. For the restricted rotational motion, the dynamics of the macromolecules can now be characterized in terms of a rotational diffusion coefficient as well as a radial distribution functions. Detailed computations for the rotational diffusion coefficient and the distribution functions have been carried out for HOOKEAN, finitely extensible nonlinear elastic, and a DNA type bead-bead interaction.

Experimental results are presented for the scattering of well-defined beams of molecular oxygen incident on clean Al(111). The data consist of scattered angular distributions measured as a function of incident angle, and for fixed incident angle, the dependence on surface temperature of the angular distributions. The measurements are interpreted in terms of a scattering theory that treats the exchange of energy between the translational and rotational motions of the molecule and the phonons of the surface using classical dynamics. The dependence of the measured angular distributions on incident beam angle and temperature is well explained by the theory. Rotational excitation and quantum excitation of the O(2) internal stretching mode are briefly discussed.

A computational methodology is presented that is designed to model, at a coarse-grained level, the mesoscale dynamics of fluids and potentially other forms of soft matter. Within a molecular dynamics simulation, "ghost" particles of a specific size, corresponding to the fundamental length-scale of coarse-graining, are used as micro-probes designed to respond to local mesoscale fluid flows and stress gradients. A subsequent coarse-grained model is then developed that incorporates both the coarse-grained mesoscale dynamics and isothermal compressibility of the original microscopic system. The method is applied to water and methanol. A contrast with dissipative particle dynamics (DPD) is also presented.

Molecular dynamics simulations of liquid water near the external surface of a carbon nanotube bundle are presented. Flexible simple point charge and Lennard-Jones potentials have been chosen to model water–water and water–carbon forces, respectively. It has been recently shown that such a system suffers a first-order phase transition between low- and high-density phases. Hydrogen bonding, diffusive behavior, rotational and vibrational motions are analyzed in the low- and high-density regimes.

HArF and HKrF are chemically bound rare-gas compounds that have been produced by photolysis of HF and subsequent thermal annealing in the respective rare-gas matrices. In this paper we present a computational study of the delayed, thermally induced formation of these molecules in the matrix. Using realistic potentials for the molecular and guest–host interactions, the potential energy along the minimum energy paths for formation is evaluated, and thermal transition rates are computed using a Monte Carlo transition state method. A closely packed, dissociated configuration of the molecular fragments is found to play an important role, both as the possible trapping site of the photolyzed fragments, and as an intermediate structure for diffusion-controlled formation. The computed threshold temperatures of formation for the HArF and HKrF molecules at different matrix sites are in good agreement with experimental findings and with previous site assignments for these molecules.

The dynamics of supercooled liquid argon is investigated via a specific correlation function ΔB. Its time behavior is well reproduced by taking into account the separate contributions of an Enskog-type diffusive part and of damped oscillations of vanishing time integral (nondiffusive part). The implications on the velocity correlation function (VCF) are investigated. Phononlike oscillations, also present in the crystal, can explain the first negative lobe and the subsequent shoulder of the VCF. The slow decay of ΔB after the fast dynamics (t

A detailed and comprehensive study of the dynamics has been performed using quasiclassical trajectory calculations on a recent version of the ground 1 1A′ potential energy surface (PES) [M. T. Martinez et al., Phys. Chem. Chem. Phys. 2, 589 (2000)] for this system. This PES was shown to account very well for the various experimental results available for the HOCl system. It has been found that this reaction occurs following different mechanisms depending on whether the HClO, HOCl, or both wells are visited in the course of the reaction. The different scalar and vector properties are strongly dependent on the type of mechanism through which a reaction takes place. Calculations have also been carried out to determine the distribution of collision times for each of the different mechanisms, and the time evolution of the differential cross section. For both reaction chemical channels the backward scattering is delayed with respect to the appearance of forward scattering. Although this reaction has been consi...

Relaxation in supercooled liquids above their glass transition and below the onset temperature of “slow” dynamics involves the correlated motion of neighboring particles. This correlated motion results in the appearance of spatially heterogeneous dynamics or “dynamical heterogeneity.” Traditional two-point time-dependent density correlation functions, while providing information about the transient “caging” of particles on cooling, are unable to provide sufficiently detailed information about correlated motion and dynamical heterogeneity. Here, we study a four-point, time-dependent density correlation function g4(r,t) and corresponding “structure factor” S4(q,t) which measure the spatial correlations between the local liquid density at two points in space, each at two different times, and so are sensitive to dynamical heterogeneity. We study g4(r,t) and S4(q,t) via molecular dynamics simulations of a binary Lennard-Jones mixture approaching the mode coupling temperature from above. We find that the correl...

We present a generalized Langevin equation for the dynamics of semiflexible polymer chains of finite size in a dynamically heterogeneous fluid. Local and global dynamical properties, calculated in the framework of this approach, display anomalous behavior in agreement with experiments and computer simulations. The presence of heterogeneous dynamics induces non-Fickian center-of-mass diffusion and an anomalous slowdown of intramolecular modes of motion. Intermolecular interactions mostly perturb lowest-index modes, which correspond to polymer global dynamics. Internal polymer stiffness induces anomalies in the relaxation of highest-index modes, which characterize local dynamics and monomer diffusion.

Ab initio molecular dynamics (AIMD) simulations are performed for studying the S0→T1 excitation dynamics of psoralen compounds; namely, nonsubstituted psoralen, 5-methoxypsoralen (5-MOP), and 8-methoxypsoralen (8-MOP). The density functional theory calculations at the B3LYP/D95V level are used for evaluating the atomic forces in every AIMD step. The specific behavior of 8-MOP in the T1 state, which has been reported by the experimental study, is found to be due to a unique open-ring structure, which leads to a different spin distribution in comparison with the cases of psoralen and 5-MOP and further to a crossing between the S0 and T1 states.

Poly(p-phenylene vinylene) (PPV) has shown a great potential for electro-optical applications due to its electroluminescent and semiconducting properties. Such properties are directly related with the polymer chain conformation and dynamics. Then, it is important to understand in detail the local chain motions. In this work, three 13C solid-state magic-angle-spinning (MAS) exchange NMR techniques were used to study conformational dynamics of phenylene rings in PPV. The standard 2D MAS exchange experiment was used to identify exchange processes between equivalent and nonequivalent sites. Centerband-only detection of exchange (CODEX) experiments were applied to determine the amplitude of the phenylene ring flips and small-angle oscillations. Additionally, a new version of the CODEX technique, which allows for the selective observation of segments executing exchange between non-equivalent sites, is demonstrated and applied to determine the flipping fractions and the activation energies of the phenylene ring ...

The dynamics of dissolved long-chain macromolecules are different in highly confined environments than in bulk solution. A computational method is presented here for detailed prediction of these dynamics, and applied to the behavior of ∼1–100 μm DNA in micron-scale channels. The method is comprised of a self-consistent coarse-grained Langevin description of the polymer dynamics and a numerical solution of the flow generated by the motion of polymer segments. Diffusivity and longest relaxation time show a broad crossover from free-solution to confined behavior centered about the point H≈10Sb, where H is the channel width and Sb is the free-solution chain radius of gyration. In large channels, the diffusivity is similar to that of a sphere diffusing along the centerline of a pore. For highly confined chains (H/Sb≪1), Rouse-type molecular weight scaling is observed for both translational diffusivity and longest relaxation time. In the highly confined region, the scaling of equilibrium length and relaxation t...

A mode-coupling treatment of nonpolar solvation dynamics in supercritical fluids is presented. Both neat fluids and dilute attractive supercritical solutions are considered. The equilibrium solvation time correlation function for the solute fluctuating transition frequency is obtained from the mode-coupling theory method and from molecular dynamics simulations. Theory is shown to be in good agreement with simulation for all solvent thermodynamic conditions studied. The microscopic origins of the density dependence of the time correlation function are discussed.

The effect of the nondiffusional short-time liquid dynamics on the kinetics of an irreversible bimolecular solution reaction (A+B→products) is investigated using a non-Markovian Smoluchowski approach. It is shown that due to the convolution-type basic equation in this concept, asymptotic rate coefficient predictions can be deduced from exact results of the Smoluchowski–Collins–Kimball theory. For the case that only the inertial effect plays a significant part in the nondiffusional reactant pair dynamics, an asymptotic short-time expansion of the rate coefficient was derived in this way. It explicitly indicates as a new reaction-kinetic result how the rate coefficient in the short-time region depends on the AB potential of mean force. Specified for the conditions of contact reactions in a simple hard-sphere fluid, the kinetic predictions of the new concept are compared with the results of other approaches.

Polymer translocation through a nanopore in a membrane investigated theoretically. Recent experiments on voltage-driven DNA and RNA translocations through a nanopore indicate that the size and geometry of the pore are important factors in polymer dynamics. A theoretical approach is presented which explicitly takes into account the effect of the nanopore length and diameter for polymer motion across the membrane. It is shown that the length of the pore is crucial for polymer translocation dynamics. The present model predicts that for realistic conditions (long nanopores and large external fields) there are two regimes of translocation depending on polymer size: for polymer chains larger than the pore length, the velocity of translocation is nearly constant, while for polymer chains smaller than the pore length the velocity increases with decreasing polymer size. These results agree with experimental data., Comment: 14 pages, 5 figures

Picosecond nonlinear absorption dynamics of neutral metal-dithiolenes belonging to the general class [M(R,R′timdt)2] (M=Ni, Pd, Pt; R,R′ timdt=monoreduced form of disubstituted imidazolidine-2,4,5-trithione) has been investigated at λ=1064 nm using the pump–probe technique. Both central metal ion M and substituents R,R′ have been found to strongly influence the temporal evolution of the absorption saturation. In particular, it has been observed that the intersystem crossing rate always increases by a factor ∼1.5 when changing the central metal from Pd to Pt. The mechanisms leading to the measured dynamics have been explained using a multilevel rate equation analysis, based on the results of relativistic time-dependent density functional calculations.

We test a theory for the long time conformational dynamics of the penta-peptide Met-enkephalin by comparison with the explicit solvent molecular dynamics and implicit solvent Langevin dynamics simulations described earlier. Using the requisite equilibrium averages computed from these simulations and friction coefficients evaluated from shorter simulations obtained with the Pastor–Karplus scheme, the generalized Rouse and mode-coupling theory (MCT) generate a variety of time-correlation functions that probe both local and global dynamics. The comparison between different levels of MCT calculations demonstrates that the smallest eigenvalues (corresponding to the relaxation rates of the slowest modes) are insensitive to the choice of the high frequency coupled modes. Compared with the direct simulations, the MCT time correlation functions for the dynamics involving the motion of certain rigid groups, such as end-to-end, interphenyl vector or certain vectors between bonded backbone atoms, often exhibit a too ...

Molecular Dynamics simulations are used to explore the effect of severe –1 nanometer– confinement on the short-time dynamics of poly(ethylene oxide) (PEO). Bulk and intercalated systems have been atomistically modeled to comparatively illustrate their differences. In particular, we aim to trace the molecular level mechanisms responsible for the counter intuitive distribution of relaxation times recorded by solid state 2H NMR for the C–H bond reorientations in confinements. Computer simulations complement the experiments and reveal that factors such as local density inhomogeneities, proximity of Li+, and disorder in the system, combine to determine the PEO segmental dynamics. In contrast with the respective bulk PEO systems, where a clear transition from distinct solid to liquid like dynamics takes place with increasing temperatures, for the nanoscopically confined chains there persists a coexistence of fast and slow segmental relaxations over the same temperature range.