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Studies have shown that pyramidal neurons are significant in regulating seizures. Based on this, we employ a modified corticothalamic model to investigate the effect of magnetic flow on seizures by adding magnetic flow to pyramidal neurons. We first separately explore the effect of the excitatory projection ( C EIN - PY ) from the excitatory interneurons (EIN) to the pyramidal neuronal population (PY), the inhibitory projection ( C IN - PY ) from the inhibitory interneurons (IN) to PY, and the excitatory projection ( C TC - PY ) from the thalamic relay nucleus (TC) to PY on the epilepsy under electromagnetic induction. The findings indicate that electromagnetic induction has two sides. On the one hand, the strong electromagnetic induction facilitates the elimination of seizures induced by pathways EIN–PY and IN–PY. On the other hand, for the seizures caused by pathway TC–PY, the electromagnetic induction triggers the system to shift from clonic seizures to spike and wave discharges (SWDs), meanwhile widens the spectrum of seizure manifestations. Furthermore, we use bifurcation analysis to obtain the dynamical mechanisms behind the transitions of discharge states, including fold limit cycle bifurcations, subcritical and supercritical Hopf bifurcations. It may provide insights into the significance of electromagnetic induction in the treatment of epilepsy. [ABSTRACT FROM AUTHOR]

The transiting mechanism of abnormal brain functional activities, such as the epileptic seizures, has not been fully elucidated. In this study, we employ a probabilistic neural network model to investigate the impact of negative regulation, including negative connections and negative inputs, on the dynamical transition behavior of network dynamics. It is observed that negative connections significantly influence the transition behavior of the network, intensifying the oscillation of discharge probability, corresponding to uneven discharge and epileptic states. Negative inputs, within a certain range, exhibited a similar impact on the dynamic state of the network as negative connections, enhancing network oscillations and resulting in higher fragility. However, larger negative inputs can led to the disappearance of oscillations in the discharge probability, indicating a maintenance of lower fragility. We speculate that negative regulation may be an indispensable factor in the occurrence of epileptic seizures, and future research should give it due consideration. [ABSTRACT FROM AUTHOR]

Temporal lobe epilepsy (TLE) is thought to be associated with neuronal hyperexcitability in the hippocampal-entorhinal cortical (EC) circuit. Due to the complexity of the hippocampal-EC network connections, the biophysical mechanisms of the different circuits in epilepsy generation and propagation are still not fully established. In this work, we propose a hippocampal-EC neuronal network model to explore the mechanism of epileptic generation. We demonstrate that enhanced excitability of pyramidal neurons in cornu ammonis 3 (CA3) can drive hippocampal-EC to produce a transition from background to seizure state and cause exaggerated phase-amplitude coupling (PAC) phenomenon of theta modulated high-frequency oscillations (HFO) in CA3, cornu ammonis 1 (CA1), dentate gyrus, and EC. Interestingly, PAC strength indirectly responds to the degree of CA3 pyramidal (PY) neuron hyperexcitability, suggesting that PAC can be used as a potential marker of seizures. Furthermore, we find that enhanced synaptic connectivity of mossy cells to granule cells and CA3 PY neurons drives the system to produce epileptic discharges. These two channels may play a key role in mossy fiber sprouting. In particular, the PAC phenomenon of delta-modulated HFO and theta-modulated HFO can be generated according to the different degrees of moss fiber sprouting. Finally, the results suggest that hyperexcitability of stellate cells in EC can lead to seizures, which supports the argument that EC can act as an independent source of seizures. Overall, these results highlight the key role of different circuits in seizures, providing a theoretical basis and new insights into the generation and propagation of TLE.

This article concerns the dynamical transitions of the stochastic Swift-Hohenberg equation with multiplicative noise on a two-dimensional domain (-L, L) × (-L, L). With α and L regarded as parameters, we show that the approximate reduced system corresponding to the invariant manifold undergoes a stochastic pitchfork bifurcation near the critical points, and the impact of noise on stochastic bifurcation of the Swift-Hohenberg equation. We find the approximation representation of the manifold and the corresponding reduced systems for stochastic Swift-Hohenberg equation when L2 and √ 2L1 are close together. [ABSTRACT FROM AUTHOR]

Temporal lobe epilepsy (TLE) is thought to be associated with neuronal hyperexcitability in the hippocampal-entorhinal cortical (EC) circuit. Due to the complexity of the hippocampal-EC network connections, the biophysical mechanisms of the different circuits in epilepsy generation and propagation are still not fully established. In this work, we propose a hippocampal-EC neuronal network model to explore the mechanism of epileptic generation. We demonstrate that enhanced excitability of pyramidal neurons in cornu ammonis 3 (CA3) can drive hippocampal-EC to produce a transition from background to seizure state and cause exaggerated phase-amplitude coupling (PAC) phenomenon of theta modulated high-frequency oscillations (HFO) in CA3, cornu ammonis 1 (CA1), dentate gyrus, and EC. Interestingly, PAC strength indirectly responds to the degree of CA3 pyramidal (PY) neuron hyperexcitability, suggesting that PAC can be used as a potential marker of seizures. Furthermore, we find that enhanced synaptic connectivity of mossy cells to granule cells and CA3 PY neurons drives the system to produce epileptic discharges. These two channels may play a key role in mossy fiber sprouting. In particular, the PAC phenomenon of delta-modulated HFO and theta-modulated HFO can be generated according to the different degrees of moss fiber sprouting. Finally, the results suggest that hyperexcitability of stellate cells in EC can lead to seizures, which supports the argument that EC can act as an independent source of seizures. Overall, these results highlight the key role of different circuits in seizures, providing a theoretical basis and new insights into the generation and propagation of TLE. [ABSTRACT FROM AUTHOR]

Epileptic seizures have spatial features related to the propagation of seizure waves. As the main characteristic of absence seizures, 2–4 Hz spike-wave discharges (SWDs) originate from the cortices and are maintained by the thalamus. In this study, we explore the onset and propagation effect of absence seizures based on a thalamocortical model. First, we develop a two-compartment model and consider the autapse of the thalamic reticular nucleus as a crucial parameter to investigate transition behaviors. Moreover, we present dynamical mechanisms through bifurcation analysis. Simulation results show that the absence seizures can be induced and advanced as the coupling strength increases. Second, we investigate excitatory and inhibitory coupling functions in a three-compartment model. Our research indicates that the excitatory coupling function can lead to SWDs when all the compartments are initially saturated. In the process of propagation, excitatory coupling also gives rise to SWDs in normal compartments, whereas inhibitory coupling plays a limited role. Finally, we reproduce the above results in a 10-compartment model and verify the robustness against the variation of the number of modules. This work may shed new light on the field of seizure propagation and provide potential dynamical mechanisms. [ABSTRACT FROM AUTHOR]

Epilepsy is believed to be associated with the abnormal synchronous neuronal activity in the brain, which results from large groups or circuits of neurons. In this paper, we choose to focus on the temporal lobe epilepsy, and establish a cortex network of multiple coupled neural populations to explore the epileptic activities under electromagnetic induction. We demonstrate that the epileptic activities can be controlled and modulated by electromagnetic induction and coupling among regions. In certain regions, these two types of control are observed to show exactly reverse effects. The results show that the strong electromagnetic induction is conducive to eliminating the epileptic seizures. The coupling among regions has a conduction effect that the previous normal background activity of the region gives way to the epileptic discharge, owing to coupling with spike wave discharge regions. Overall, these results highlight the role of electromagnetic induction and coupling among the regions in controlling and modulating epileptic activities, and might provide novel insights into the treatments of epilepsy. [ABSTRACT FROM AUTHOR]

We study the dynamical transitions of the stochastic Swift-Hohenberg equation with multiplicative noise on a one-dimensional domain (0 , L). With α and the length of the domain L regarded as parameters, we show that the approximate reduced system corresponding to the invariant manifold undergoes a stochastic pitchfork bifurcation near the critical points, and analyze the case when the bifurcation points nearly coincide. We show the impact of noise on stochastic bifurcation of the Swift-Hohenberg equation. [ABSTRACT FROM AUTHOR]

Complex bursting patterns and the bifurcation generation mechanism are investigated in the parametrically and externally driven Φ6-van der Pol system. Five different bursting types, i.e. symmetric ‘subHopf / homoclinic’ bursting, symmetric ‘subHopf / fold-cycle’ bursting via ‘subHopf / subHopf’ hysteresis loop, symmetric ‘subHopf / fold-cycle’ bursting, ‘subHopf / subHopf’ bursting and ‘fold / fold’ bursting, are explored. First, the mechanism of symmetric ‘subHopf / fold-cycle’ bursting via ‘subHopf / subHopf’ hysteresis loop is revealed. Then, based on the two-parameter bifurcation analysis, dynamical evolutions of the symmetric bursting are presented. Different clusters appear when the parameter changes, leading to different patterns of bursting oscillations. In addition, we find that the jumping phenomenon depends not only on the fold bifurcation, but also on the subcritical Hopf bifurcation. Finally, numerical simulations are presented to demonstrate the correctness of the research. [ABSTRACT FROM AUTHOR]

We propose an exact solution to a linear two-level system with the existence of a special hyperbolic secant external field and elucidate its transition dynamics. We then extend the model to the nonlinear case and show that the nonlinearity will significantly affect the transition dynamics. As nonlinearity increases, Landau–Zener–Stückelberg–Majorana interference fringes can be constructive and the up energy level in the adiabatic limit splits into three levels. For fast-sweeping fields, we derive an analytic expression for dynamics transition under the stationary phase approximation and find that transition probability will be blocked as the nonlinearity intensity is much larger than the external field frequency, which agrees with the numerical result. [ABSTRACT FROM AUTHOR]

In this paper, we study the dynamical transition and chaos for a five‐dimensional Lorenz system. Based on the eigenvalue analysis, the principle of exchange of stabilities conditions is obtained. By using the dynamical transition theory, three different types of dynamical transition for the five‐dimensional Lorenz system are derived. More precisely, when the control parameter r=1, the system has a continuous transition and bifurcates to two stable steady states. As r further increases, the system undergoes two successive transitions. That is, under some condition, the transition is continuous and a stable limit cycle is bifurcated; if not, the system undergoes a jump transition and an unstable periodic orbit occurs. Especially, the chaotic orbits occur when r=36.91. Finally, numerical results are given to illustrate our theoretical analysis. [ABSTRACT FROM AUTHOR]

We study the loss, recovery, and preservation of differentiability of time-dependent large deviation rate functions. This study is motivated by mean-field Gibbs-non-Gibbs transitions. The gradient of the rate-function evolves according to a Hamiltonian flow. This Hamiltonian flow is used to analyze the regularity of the time-dependent rate function, both for Glauber dynamics for the Curie-Weiss model and Brownian dynamics in a potential. We extend the variational approach to this problem of time-dependent regularity in order to include Hamiltonian trajectories with a finite lifetime in closed domains with a boundary. This leads to new phenomena, such a recovery of smoothness. We hereby create a new and unifying approach for the study of mean-field Gibbs-non-Gibbs transitions, based on Hamiltonian dynamics and viscosity solutions of Hamilton-Jacobi equations. [ABSTRACT FROM AUTHOR]

This study examines the Hopf (double Hopf) bifurcations and transitions of two dimensional quasi-geostrophic (QG) flows that model various large-scale oceanic and atmospheric circulations. Using the Kolmogorov function to represent an external forcing in the tropical region, it is shown that the equilibrium of the QG model loses its stability if the combination of the Rossby number, the Ekman number, and the eddy viscosity satisfies a specific condition. Further use of the center manifold technique reveals two different types of the dynamical transition from either a pair of simple complex eigenvalues or a double pair of complex conjugate eigenvalues. These dynamical transitions are confirmed in the numerical analyses of the QG dynamics at the equilibrium, which capture Hopf (double Hopf) bifurcations due to the existence of a nonzero imaginary part of the first eigenvalue. The transition from a pair of simple complex eigenvalues is of particular interest, because it indicates the existence of a stable periodic pattern that is similar to atmospheric easterly waves and related tropical cyclone formation in the tropical atmosphere. [ABSTRACT FROM AUTHOR]

Considering the disinhibition circuit between inhibitory neuronal populations with different time scales in cortical neural networks, here we propose a novel model to describe the occurrences and transitions of epilepsy waveforms. With the model we can successfully simulate poly-spike complexes, which are common in electrophysiological experiments and focal epilepsy patients. Meanwhile, we focus on the dynamic transitions between epilepsy waveforms and normal state and are devoted to exploring effective electrical stimulation strategies. Results show that disinhibition can induce an epileptic bidirectional transition, which is from spike and wave discharges, to poly-spike complexes and then to low-voltage rapid discharge activity, or it is reversed. And fascinating dynamical transition behaviors can be induced by varying average inhibitory synaptic gain. Interestingly, after applying two different control signals (deep brain stimulation and oscillatory input) to the system, all epilepsy waveforms can be suppressed or even eliminated. Results shed light on the pathophysiological mechanisms of epilepsy and guide clinical treatment from a theoretical viewpoint. [ABSTRACT FROM AUTHOR]

Systems of dense spheres interacting through very short-ranged attraction are known from theory, simulations and colloidal experiments to exhibit dynamical reentrance. Their liquid state can thus be fluidized at higher densities than possible in systems with pure repulsion or with long-ranged attraction. A recent mean-field, infinite-dimensional calculation predicts that the dynamical arrest of the fluid can be further delayed by adding a longer-ranged repulsive contribution to the short-ranged attraction. We examine this proposal by performing extensive numerical simulations in a three-dimensional system. We first find the short-ranged attraction parameters necessary to achieve the densest liquid state, and then explore the parameter space for an additional longer-ranged repulsion that could further enhance reentrance. In the family of systems studied, no significant (within numerical accuracy) delay of the dynamical arrest is observed beyond what is already achieved by the short-ranged attraction. Possible explanations are discussed. [ABSTRACT FROM AUTHOR]

Abstract We present results from molecular dynamics simulations of a solution of water and trehalose, a cryoprotecting disaccharide, upon cooling. We focus our attention on both the dynamics of hydration water and of the trehalose. Hydration water presents two slow relaxations. One is the α relaxation typical of glass formers and the second one is a long relaxation that was also found in proteins hydration water and appears coupled to the movement of the surface of trehaloses. Below 280 K trehalose aggregates and upon further cooling we find a dynamical transition for the trehalose aggregate at around 250 K similar to the well known Protein Dynamical Transition. When this transition happens the long relaxation time has a dynamical crossover. We hypothesize that this dynamical transition is a general feature that can be found not only in proteins but also in aggregates that interact with water and that have a flexible structure. In fact this feature has already been found not only in proteins hydration water but also in a colloidal microgel. In the known cases, including the one that we present here, water enhances movements of the surface of these aggregates above a certain temperature. The temperature of this dynamical transition ranges between 260 K and 220 K in all known cases. Highlights • Trehalose hydration water dynamics has two relaxations with crossovers upon cooling. • For the alpha relaxation region the TTSP works and MCT is tested. • Atomic MSDs show crossovers coupled to the dynamical crossovers of the relaxations. • One of the MSD crossover is analogous to the Protein Dynamical Transition. • The Dynamical Transition appears to be a general feature due to water. [ABSTRACT FROM AUTHOR]

Motivated by the recent experimental findings that thalamic reticular nucleus (TRN) may be a pacemaker of absence seizures, we explore whether changes in the level of TRN activation can induce absence seizures by using a coupled thalamocortical model. We first simulate different firing states by considering the interaction of pathway between cortical excitatory pyramidal neuronal population (PY)–TRN and specific relay nucleus (SRN)–TRN. By simultaneously increasing the coupling strength of each of these pathways, we can reproduce the absence seizures, which indicates that epileptic seizures may be caused by activating the TRN. We further infer that the TRN may be an epileptogenic focus. Following this, different stimulation strategies, including deep brain stimulation, 1:0 coordinated reset stimulation (CRS) and 3:2 CRS, are applied in TRN. By qualitatively analyzing the efficacy of three different stimulation methods, we find that 3:2 CRS is a more effective and safe method to control absence seizures in the first compartment, for which we then further explore the impact of 3:2 CRS in the second compartment. The results show that the additional stimulation in the second compartment also can lead to a considerable decrease in the spike-and-wave discharges (SWD) oscillation region. Therefore, we conclude that TRN-3:2 CRS is an optimal electrical stimulation method for our modeling and simulation studies. Furthermore, we hope that these numerical simulation results can provide some references for the treatment of real epilepsy patients in the future. [ABSTRACT FROM AUTHOR]

In temporal lobe epilepsy (TLE), the variation of chemical receptor expression underlies the basis of neural network activity shifts, resulting in neuronal hyperexcitability and epileptiform discharges. However, dynamical mechanisms involved in the transitions of TLE are not fully understood, because of the neuronal diversity and the indeterminacy of network connection. Hence, based on Hodgkin–Huxley (HH) type neurons and Pinsky–Rinzel (PR) type neurons coupling with glutamatergic and GABAergic synaptic connections respectively, we propose a computational framework which contains dentate gyrus (DG) region and CA3 region. By regulating the concentration range of N-methyl-D-aspartate-type glutamate receptor (NMDAR), we demonstrate the pyramidal neuron can generate transitions from interictal to seizure discharges. This suggests that enhanced endogenous activity of NMDAR contributes to excitability in pyramidal neuron. Moreover, we conclude that excitatory discharges in CA3 region vary considerably on account of the excitatory currents produced by the excitatory pyramidal neuron. Interestingly, by changing the backprojection connection, we find that glutamatergic type backprojection can promote the dominant frequency of firings and further motivate excitatory counterpropagation from CA3 region to DG region. However, GABAergic type backprojection can reduce firing rate and block morbid counterpropagation, which may be factored into the terminations of TLE. In addition, neuronal diversity dominated network shows weak correlation with different backprojections. Our modeling and simulation studies provide new insights into the mechanisms of seizures generation and connectionism in local hippocampus, along with the synaptic mechanisms of this disease.

Dynamical transitions, already found in the high- and low-density phases of the Totally Asymmetric Simple Exclusion Process and a couple of its generalizations, are singularities in the rate of relaxation towards the Non-Equilibrium Stationary State (NESS), which do not correspond to any transition in the NESS itself. We investigate dynamical transitions in the one-dimensional Katz−Lebowitz−Spohn model, a further generalization of the Totally Asymmetric Simple Exclusion Process where the hopping rate depends on the occupation state of the 2 nodes adjacent to the nodes affected by the hop. Following previous work, we choose Glauber rates and bulk-adapted boundary conditions. In particular, we consider a value of the repulsion which parameterizes the Glauber rates such that the fundamental diagram of the model exhibits 2 maxima and a minimum, and the NESS phase diagram is especially rich. We provide evidence, based on pair approximation, domain wall theory and exact finite size results, that dynamical transitions also occur in the one-dimensional Katz−Lebowitz−Spohn model, and discuss 2 new phenomena which are peculiar to this model.

Deep brain stimulation (DBS) can play a crucial role in themodulation of absence seizures, yet relevant biophysical mechanisms are not completely established. In this paper, on the basis of a biophysical mean-field model, we investigate a typical absence epilepsy activity by introducing slow kinetics of GABAB receptors on thalamus reticular nucleus (TRN).We find that the region of spike and slow-wave discharges (SWDs) can be reduced greatly when we add the DBS to TRN. Furthermore, we systematically explore how the corresponding stimulation parameters including frequency, amplitude and positive input duration suppress the SWDs under certain conditions. It is shown that the SWDs can be controlled as key stimulation parameters are suitably chosen. The results in this paper can be helpful for researchers to understand the thalamus stimulation in treating epilepsy patients, and provide theoretical basis for future experimental and clinical studies. [ABSTRACT FROM AUTHOR]

We consider a system of real-valued spins interacting with each other through a mean-field Hamiltonian that depends on the empirical magnetisation of the spins. The system is subjected to a stochastic dynamics where the spins perform independent Brownian motions. Using large deviation theory we show that there exists an explicitly computable crossover time t c ∈ [ 0 , ∞ ] from Gibbs to non-Gibbs. We give examples of immediate loss of Gibbsianness ( t c = 0 ), short-time conservation and large-time loss of Gibbsianness ( t c ∈ ( 0 , ∞ ) ), and preservation of Gibbsianness ( t c = ∞ ). Depending on the potential, the system can be Gibbs or non-Gibbs at the crossover time t = t c . [ABSTRACT FROM AUTHOR]

We continue our study of Gibbs-non-Gibbs dynamical transitions. In the present paper we consider a system of Ising spins on a large discrete torus with a Kac-type interaction subject to an independent spin-flip dynamics (infinite-temperature Glauber dynamics). We show that, in accordance with the program outlined in van Enter et al. (Moscow Math. J. 10:687-711, ), in the thermodynamic limit Gibbs-non-Gibbs dynamical transitions are equivalent to bifurcations in the set of global minima of the large-deviation rate function for the trajectories of the empirical density conditional on their endpoint. More precisely, the time-evolved measure is non-Gibbs if and only if this set is not a singleton for some value of the endpoint. A partial description of the possible scenarios of bifurcation is given, leading to a characterization of passages from Gibbs to non-Gibbs and vice versa, with sharp transition times. Our analysis provides a conceptual step-up from our earlier work on Gibbs-non-Gibbs dynamical transitions for the Curie-Weiss model, where the mean-field interaction allowed us to focus on trajectories of the empirical magnetization rather than the empirical density. [ABSTRACT FROM AUTHOR]

Highlights: [•] The role played by the instrumental energy resolution in neutron scattering is presented. [•] The effect of natural bioprotectants on protein dynamics is shown. [•] A connection between the protein dynamical transition and the fragile-to-strong dynamical crossover is formulated. [Copyright &y& Elsevier]

Abstract: This Letter develops a new staggered car-following model taking into consideration lateral separation effects. Time-to-collision, calculated using visual angle variables, is introduced to describe the lateral separation distance and improve the optimal velocity model. The analytical and numerical results show that the stability of traffic flow can gradually be enhanced with the increase of lateral separation effects. The asymmetry property of traffic flow is also investigated using the new model. The results imply that incorporating lateral separation effects into the car-following model leads to the suppression of traffic jams and greatly enhances the realism of the model. [Copyright &y& Elsevier]

Abstract: We study the dynamical behavior and transitions of shuttle buses in a transportation system reducing energy consumption. We present the nonlinear-map model for the dynamics of buses. The motion of shuttle buses depends on the loading parameter and the number. The dependence of the fixed points on the loading parameter is derived. The dynamical transitions occur at stages with increasing the value of loading parameter. At the dynamical transition point, the motion of buses changes from a stable (an unstable) state to an unstable (a stable) state. The shuttle buses display periodic motions with various periods in the unstable state. In the unstable state, the number of riding passengers fluctuates complexly with varying trips. [Copyright &y& Elsevier]

Abstract: We study the traffic behavior when a vehicle changes from the first lane to the second lane on a two-lane highway. We apply the optimal velocity model to the vehicular motion. If the incoming vehicle does not decelerate successfully, it crashes into the vehicle ahead. On the other hand, if the headway between the incoming vehicle and the vehicle behind on the second lane is not long sufficiently, the rear vehicle may come into collision with the incoming vehicle. The safety–collision transition occurs by changing the lane. The dynamical transition depends highly on the vehicular speed, the sensitivity, and the headway. We derive the phase diagram (or region map) for the safety–collision transition. [Copyright &y& Elsevier]

Abstract: Background: We focus on temperature- and hydration-dependence of internal molecular motions in stripped human red blood cell (RBC) vesicles, widely used as a model system for more complex biomembranes. Methods: We singled out picosecond local motions of the non-exchangeable hydrogen atoms of RBC vesicles by performing elastic and quasielastic incoherent neutron scattering measurements in dry and heavy water (D2O)-hydrated RBC powders. Results: In dry stripped RBCs, hydrogen motions remained harmonic all along the measured temperature range (100–310K) and mean–square displacements (MSDs) exhibited no temperature transition up to 310K. In contrast, MSDs of hydrated stripped RBCs (h ≈0.38g D2O/g dry powder) exhibited a pronounced transition near 260K, with the sharp rise of anharmonic diffusive motions of hydrogen atoms. This transition at ~260K was correlated with both the onset of nonvibrational (harmonic and nonharmonic) motions and the melting of crystallized hydration water. General significance: In conclusion, we have shown that MSDs in human RBC vesicles are temperature-and hydration-dependent. These results provide insight into biomembrane internal dynamics at picosecond timescale and nanometer length scale. Such motions have been shown to act as the “lubricant” of larger conformational changes on a slower, millisecond timescale that are necessary for important biological processes. [ABSTRACT FROM AUTHOR]

Abstract: The main aim of the present work is to investigate the dynamical effects of the addition of disaccharides to hydrated lysozyme. The Self-Distribution-Function procedure is at first applied on Elastic Incoherent Neutron Scattering data obtained by the IN13 spectrometer on trehalose/H2O and sucrose/H2O where it highlights a different Q-dependence for the two disaccharides. Then a quantitative analysis of the Mean Square Displacement of lysozyme/trehalose/H2O and of lysozyme/sucrose/H2O from Elastic Incoherent Neutron Scattering data obtained by the IN10 spectrometer is presented. It is shown how the resolution function gives rise to a time integration of a given time-dependent Mean Square Displacement function. Furthermore the analysis shows that the protein dynamical transition, registered at a temperature value of about T=200–220K in the H2O hydrated lysozyme sample, is inhibited by the addition of the disaccharides. [ABSTRACT FROM AUTHOR]

We have measured spectra of the absorption coefficient and refractive index of hen egg white lysozyme in the wavenumber region from 7 cm-1 to 50 cm-1 by terahertz (THz) time-domain spectroscopy. From comparison with the results of the inelastic neutron scattering experiment it is concluded that analysis of the THz spectra provides information on the vibrational density of states. We studied temperature dependence of the THz spectra as well as hydration effect on them to discuss structural fluctuation of the protein. We observed dynamical transition at around 210 K for lysozyme. [ABSTRACT FROM AUTHOR]

Abstract: In order to examine the properties specific to the folded protein, the effect of the conformational states on protein dynamical transition was studied by incoherent elastic neutron scattering for both wild type and a deletion mutant of staphylococcal nuclease. The deletion mutant of SNase which lacks C-terminal 13 residues takes a compact denatured structure, and can be regarded as a model of intrinsic unstructured protein. Incoherent elastic neutron scattering experiments were carried out at various temperature between 10 K and 300 K on IN10 and IN13 installed at ILL. Temperature dependence of mean-square displacements was obtained by the q-dependence of elastic scattering intensity. The measurements were performed on dried and hydrated powder samples. No significant differences were observed between wild type and the mutant for the hydrated samples, while significant differences were observed for the dried samples. A dynamical transition at ∼140 K observed for both dried and hydrated samples. The slopes of the temperature dependence of MSD before transition and after transition are different between wild type and the mutant, indicating the folding induces hardening. The hydration water activates a further transition at ∼240 K. The behavior of the temperature dependence of MSD is indistinguishable for wild type and the mutant, indicating that hydration water dynamics dominate the dynamical properties. [Copyright &y& Elsevier]

Abstract: The protein dynamical transition and its connection with the liquid-glass transition (GT) of hydration water and aqueous solvents are reviewed. The protein solvation shell exhibits a regular glass transition, characterized by steps in the specific heat and the thermal expansion coefficient at the calorimetric glass temperature T G ≈170 K. It implies that the time scale of the structural α-relaxation has reached the experimental time window of 1–100 s. The protein dynamical transition, identified from elastic neutron scattering experiments by enhanced amplitudes of molecular motions exceeding the vibrational level [1], probes the α-process on a shorter time scale. The corresponding liquid-glass transition occurs at higher temperatures, typically 240 K. The GT is generally associated with diverging viscosities, the freezing of long-range translational diffusion in the supercooled liquid. Due to mutual hydrogen bonding, both, protein- and solvent relaxational degrees of freedom slow down in paralled near the GT. However, the freezing of protein motions, where surface-coupled rotational and librational degrees of freedom are arrested, is better characterized as a rubber-glass transition. In contrast, internal protein modes such as the rotation of side chains are not affected. Moreover, ligand binding experiments with myoglobin in various glass-forming solvents show, that only ligand entry and exit rates depend on the local viscosity near the protein surface, but protein-internal ligand migration is not coupled to the solvent. The GT leads to structural arrest on a macroscopic scale due to the microscopic cage effect on the scale of the intermolecular distance. Mode coupling theory provides a theoretical framework to understand the microcopic nature of the GT even in complex systems. The role of the α- and β-process in the dynamics of protein hydration water is evaluated. The protein-solvent GT is triggered by hydrogen bond fluctuations, which give rise to fast β-processes. High-frequency neutron scattering spectra indicate increasing hydrogen bond braking above T G. [Copyright &y& Elsevier]

Abstract: The general trend in soft matter is to study systems of increasing complexity which are more technologically and biologically relevant. This is facilitated by the capability of quasielastic neutron scattering (QENS) to selectively probe spatially resolved dynamical modes at a molecular level. The large number of recent publications using QENS for investigating complex and multi-component soft matter systems, serves as recognition of the suitability of this technique by the scientific community. Exploiting its complementarity with molecular dynamics (MD) simulations and other experimental techniques is the basis of a successful methodology for this scientific challenge. We illustrate the potential of QENS with three kinds of soft materials whose structural units increase in size/complexity: lipids, polymers and biomolecules. [Copyright &y& Elsevier]

Abstract: We show how the Jarzynski relation can be exploited to analyze the nature of order–disorder, and a bifurcation type dynamical transition in terms of a response function derived on the basis of work distribution over non-equilibrium paths between two thermalized states. The validity of the response function extends over a linear as well as a nonlinear regime, and far from equilibrium situations. [Copyright &y& Elsevier]

The function and dynamics of proteins depend on their direct environment, and much evidence has pointed to a strong coupling between water and protein motions. Recently however, neutron scattering measurements on deuterated and natural-abundance purple membrane (PM), hydrated in H2O and D2O, respectively, revealed that membrane and water motions on the ns–ps time scale are not directly coupled below 260 K (Wood et al. in Proc Natl Acad Sci USA 104:18049–18054, ). In the initial study, samples with a high level of hydration were measured. Here, we have measured the dynamics of PM and water separately, at a low-hydration level corresponding to the first layer of hydration water only. As in the case of the higher hydration samples previously studied, the dynamics of PM and water display different temperature dependencies, with a transition in the hydration water at 200 K not triggering a transition in the membrane at the same temperature. Furthermore, neutron diffraction experiments were carried out to monitor the lamellar spacing of a flash-cooled deuterated PM stack hydrated in H2O as a function of temperature. At 200 K, a sudden decrease in lamellar spacing indicated the onset of long-range translational water diffusion in the second hydration layer as has already been observed on flash-cooled natural-abundance PM stacks hydrated in D2O (Weik et al. in J Mol Biol 275:632–634, ), excluding thus a notable isotope effect. Our results reinforce the notion that membrane-protein dynamics may be less strongly coupled to hydration water motions than the dynamics of soluble proteins. [ABSTRACT FROM AUTHOR]

The dynamics of hydrated proteins and of protein crystals can be studied within a wide temperature range, since the water of hydration does not crystallize at low temperature. Instead it turns into an amorphous glassy state below 200 K. Extending the temperature range facilitates the spectral separation of different molecular processes. The conformational motions of proteins show an abrupt enhancement near 180 K, which has been called a “dynamical transition”. In this contribution various aspects of the transition are critically reviewed: the role of the instrumental resolution function in extracting displacements from neutron elastic scattering data and the question of the appropriate dynamic model, discrete transitions between states of different energy versus continuous diffusion inside a harmonic well, are discussed. A decomposition of the transition involving two motional components is performed: rotational transitions of methyl groups and small scale librations of side-chains, induced by water at the protein surface. Both processes create an enhancement of the observed amplitude. The onset occurs, when their time scale becomes compatible with the resolution of the spectrometer. The reorientational rate of hydration water follows a super-Arrhenius temperature dependence, a characteristic feature of a dynamical transition. It occurs only with hydrated proteins, while the torsional motion of methyl groups takes place also in the dehydrated or solvent-vitrified system. Finally, the role of fast hydrogen bond fluctuations contributing to the amplitude enhancement is discussed. [ABSTRACT FROM AUTHOR]

We used MD simulations to investigate the dependence of the dynamics of a soluble protein, RNase A, on temperature and solvent environment. Consistent with neutron scattering data, the simulations predict that the protein undergoes a dynamical transition in both glycerol and aqueous solutions that is absent in the dry protein. The temperature of the transition is higher, while the rate of increase with temperature of the amplitudes of motion on the 100 ps timescale is lower, in glycerol versus water. Analysis of the dynamics of hydrogen bonds revealed that the protein dynamical transition is connected to the relaxation of the protein–solvent hydrogen bond network, which, in turn, is associated with solvent translational diffusion. Thus, it appears that the role of solvent dynamics in affecting the protein dynamical transition is qualitatively similar in water and glycerol. [ABSTRACT FROM AUTHOR]

Through elastic neutron scattering measurements, we investigated the thermal fluctuations of DNA enclosed by glycerol–water glassy matrices, at different levels of hydration, over the wide temperature range from 20 to 300 K. For all the samples, the extracted hydrogen mean square displacements (MSD) show a purely vibrational harmonic trend at very low temperatures, and a first onset of anharmonic dynamics above ∼100 K. Such onset is consistent with the activation of DNA methyl group rotational motions. Then, at a certain temperature T d, the MSD show a second onset of anharmonicity, which corresponds to the DNA dynamical transition. The T d values vary as a function of the hydration degree of the environment. The crucial role of the solvent mobility to activate the DNA thermal fluctuations is proposed, together with a preferential hydration effect of the DNA phosphate groups. Finally, a comparison between the average mobility of homologous samples of DNA and the lysozyme protein is considered. [ABSTRACT FROM AUTHOR]

Abstract: The dynamics of Ribonuclease A was explored in the full range of time and length-scales accessible by neutron spectroscopy, on time-of-flight, backscattering and spin-echo spectrometers. Samples were examined in dry and hydrated powder forms and in concentrated and dilute solutions. The aim of the study was an experimental characterisation of the full variety of protein dynamics arising from stabilisation forces. The results provide a benchmark against which other sample dynamics can be compared. [Copyright &y& Elsevier]

The dynamical coupling between proteins and their hydration water is important for the understanding of macromolecular function in a cellular context. In the case of membrane proteins, the environment is heterogeneous, composed of lipids and hydration water, and the dynamical coupling might be more complex than in the case of the extensively studied soluble proteins. Here, we examine the dynamical coupling between a biological membrane, the purple membrane (PM), and its hydration water by a combination of elastic incoherent neutron scattering, specific deuteration, and molecular dynamics simulations. Examining completely deuterated PM, hydrated in H2O, allowed the direct experimental exploration of water dynamics. The study of natural abundance PM in D2O focused on membrane dynamics. The temperature-dependence of atomic mean-square displacements shows inflections at 120 K and 260 K for the membrane and at 200 K and 260 K for the hydration water. Because transition temperatures are different for PM and hydration water, we conclude that ps-ns hydration water dynamics are not directly coupled to membrane motions on the same time scale at temperatures <260 K. Molecular-dynamics simulations of hydrated PM in the temperature range from 100 to 296 K revealed an onset of hydration-water translational diffusion at 200 K, but no transition in the PM at the same temperature. Our results suggest that, in contrast to soluble proteins, the dynamics of the membrane protein is not controlled by that of hydration water at temperatures <260 K. Lipid dynamics may have a stronger impact on membrane protein dynamics than hydration water. [ABSTRACT FROM AUTHOR]