arXiv subjects

Gregor Diezemann

Publications and source records attributed to Gregor Diezemann.

At least 19 recordsLinked to original sources

arXiv2026

Markov State Model for the forced unfolding of a small peptide

In typical single-molecule force spectroscopy experiments the mechanical unfolding of molecular complexes or biomolecules is studied applying a force ramp to one end of the system while the other end is kept fixed in space. The computational counterpart of this type of experiments can routinely be performed using molecular dynamics simulations with atomistic resolution. However, due to the large difference in time scales often coarse graining procedures are applied in the simulations. Most of the applied techniques do not allow to follow the atomistic details of the relevant conformational transitions due to the structural simplifications used to speed up the simulations. Here, we apply an earlier developed dynamic coarse graining technique based on Markov state modeling to a model peptidic system that does not unfold in a simple two-state manner. Using the donor-acceptor distances of the helical hydrogen bonds as collective variables and performing a dimension reduction technique allows us to construct a Markov model of the unfolding process that correctly represents the microscopic behavior of the system. The chosen example shows that the method can be used to mimick the mechanical unfolding process of systems for which the end-to-end distance does not provide a sufficient order parameter and that do not unfold in a simple cooperative manner.

cond-mat.soft↗

arXiv2024

Adaptive Resolution Force Probe Simulations: Coarse Graining in the Ideal Gas Approximation

The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental force spectroscopy, often coarse graining procedures are employed. Here, building on a previous study, we apply the adaptice resolution scheme (AdResS) to force probe molecular dynamics (FPMD) simulations using two model systems as examples. One system is the previously investigated calix[4]arene dimer that shows reversible one-step unfolding and the other example is provided by a small peptide, a $β$-alanine octamer in methanol solvent. The mechanical unfolding of this peptide proceeds via a metastable intermediate and therefore represents a first step towards a complex unfolding pathway. In addition to increasing the complexity of the relevant conformational changes we study the impact of the methodology used for coarse graining. Apart from a standard technique, the iterative Boltzmann inversion method, we apply an ideal gas approximation and therefore we replace the solvent by a non-interacting system of spherical particles. In all cases we find excellent agreement between the results of FPMD simulations performed fully atomistically and the AdResS simulations also in the case of fast pulling. This holds for all details of the unfolding pathways like the distributions of the characteristic forces and also the sequence of hydrogen-bond opening in case of the $β$-alanine octamer. Therefore, the methodology is very well suited to simulate the mechanical unfolding of systems of experimental relevance also in the presence of protic solvents.

cond-mat.soft↗

arXiv2022

Nonlinear response theory for Markov processes IV: The asymmetric double well potential model revisited

The dielectric response of non-interacting dipoles is discussed in the framework of the classical model of stochastic reorientations in an asymmetric double well potential (ADWP). In the nonlinear regime, this model exhibits some pecularities in the static response. We find that the saturation behavior of the symmetric double well potential model does not follow the Langevin function and only in the linear regime the standard results are recovered. If a finite asymmetry is assumed, the nonlinear susceptibilities are found to change the sign at a number of characteristic temperatures that depend on the magnitude of the asymmetry, as has been observed earlier for the third-order and the fifth-order response. If the kinetics of the barrier crossing in the ADWP model is described as a two-state model, we can give analytical expressions for the values of the characteristic temperatures. The results for the response obtained from a (numerical) solution of the Fokker-Planck equation for the Brownian motion in a model ADWP behaves very similar to the two-state model for high barriers. For small barriers no clearcut time scale separation between the barrier crossing process and the intra-well relaxation exists and the model exhibits a number of time scales. In this case, the frequency-dependent linear susceptibility at low temperatures is dominated by the fast intra-well transitions and at higher temperatures by the barrier crossing kinetics. We find that for nonlinear susceptibilities the latter process appears to be more important and the intra-well transitions play only role at the lowest temperatures.

cond-mat.stat-mech↗

arXiv2021

Force probe simulations using an adaptive resolution scheme

Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In force probe molecular dynamics (FPMD) simulations, one pulls one end of the molecule with a constant velocity in order to induce the relevant conformational transitions. Since the extended configuration of the system has to fit into the simulation box together with the solvent such simulations are very time consuming. Here, we apply a hybrid scheme in which the solute is treated with atomistic resolution and the solvent molecules far away from the solute are described in a coarse-grained manner. We use the adaptive resolution scheme (AdResS) that has very successfully been applied to various examples of equilibrium simulations. We perform FPMD simulations using AdResS on a well studied system, a dimer formed from mechanically interlocked calixarene capsules. The results of the multiscale simulations are compared to all-atom simulations of the identical system and we observe that the size of the region in which atomistic resolution is required depends on the pulling velocity, i.e. the particular non-equilibrium situation. For large pulling velocities a larger all atom region is required. Our results show that multiscale simulations can be applied also in the strong non-equilibrium situations that the system experiences in FPMD simulations.

cond-mat.soft↗

arXiv2018

Nonlinear response theory for Markov processes III: Stochastic models for dipole reorientations

The nonlinear response of molecular systems undergoing Markovian stochastic reorientations is calculated up to fifth order in the amplitude of the external field. Time-dependent perturbation theory is used to compute the relevant response functions as in earlier treatments (G. Diezemann, Phys. Rev. E{\bf 85}, 051502 (2012), Phys. Rev. E{\bf 96}, 022150 (2017)). Here, we consider the reorientational motion of isolated molecules and extend the existing calculations for the model of isotropic rotational diffusion to the model of anisotropic rotational diffusion and to the model of rotational random jumps. Depending on the values of some model parameters, we observe a hump in the modulus of the nonlinear susceptibility for either of these models. Interestingly, for the model of rotational random jumps, the appearance of this hump depends on the way the coupling to the external field is modelled in the master equation approach. If the model of anisotropic rotational diffusion is considered, the orientation of the diffusion tensor relative to the molecular dipole moment and additionally the amount of anisotropy in the rotational diffusion constants determine the detailed shape of the nonlinear response. In this case, the height of the observed hump is found to increase with increasing 'diffusional anisotropy'. We discuss our results in relation to the features observed experimentally in supercooled liquids.

cond-mat.soft↗

arXiv2017

Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding

We present a dynamic coarse-graining technique that allows to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSM), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately $10^{-8}$/ns to $1$/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.

cond-mat.soft↗

arXiv2017

Nonlinear response theory for Markov processes II: Fifth-order response functions

The nonlinear response of stochastic models obeying a master equation is calculated up to fifth-order in the external field thus extending the third-order results obtained earlier (G. Diezemann, Phys. Rev. E{\bf 85}, 051502 (2012)). For sinusoidal fields the $5\om$-component of the susceptibility is computed for the model of dipole reorientations in an asymmetric double well potential and for a trap model with a Gaussian density of states. For most realizations of the models a hump is found in the higher-order susceptibilities. In particular, for the asymmetric double well potential model there are two characteristic temperature regimes showing the occurence of such a hump as compared to a single characteristic regime in case of the third-order response. In case of the trap model the results strongly depend on the variable coupled to the field. As for the third-order response, the low-frequency limit of the susceptibility plays a crucial role with respect to the occurence of a hump. The findings are discussed in light of recent experimental results obtained for supercooled liquids. The differences found for the third-order and the fifth-order response indicate that nonlinear response functions might serve as a powerful tool to discriminate among the large number of existing models for glassy relaxation.

cond-mat.soft↗

arXiv2014

Nonlinear response functions in an exponential trap model

The nonlinear response to an oscillating field is calculated for a kinetic trap model with an exponential density of states and the results are compared to those for the model with a Gaussian density of states. The calculations are limited to the high temperature phase of the model. It is found that the results are qualitatively different only in a temperature range near the glass transition temperature $T_0$ of the exponential model. While for the Gaussian model the choice of the dynamical variable that couples to the field has no impact on the shape of the linear response, this is different for the exponential model. Here, it is found that also the relaxation time strongly depends on the variable chosen. Furthermore, the modulus of the frequency dependent third-order response shows either a peak or exhibits a monotonuous decay from a finite low-frequency limit to a vanishing response at high frequencies depending on the dynamical variable. For variables that give rise to a peak in the modulus it is found that its height either increases or decreases as a function of temperature, again depending on the details of the choice of the variable. The peak value of the modulus shows a scaling behavior near $T_0$. It is found that for some variables the low-frequency limit of the cubic response diverges at the glass transition temperature and also at a further temperature determined by the particular variable. A recently proposed approximation that relates the cubic response to a four-time correlation function does not give reliable results due to a wrong estimate of the low-frequency limit of the response.

cond-mat.soft↗

arXiv2014

Statistics of reversible transitions in two-state trajectories in force-ramp spectroscopy

A possible way to extract information about the reversible dissociation of a molecular adhesion bond from force fluctuations observed in force ramp experiments is discussed. For small loading rates the system undergoes a limited number of unbinding and rebinding transitions observable in the so-called force versus extension (FE) curves. The statistics of these transient fluctuations can be utilized to estimate the parameters for the rebinding rate. This is relevant in the experimentally important situation where the direct observation of the reversed FE-curves is hampered, e.g. due to the presence of soft linkers. I generalize the stochastic theory of the kinetics in two-state models to the case of time-dependent kinetic rates and compute the relevant distributions of characteristic forces. While for irreversible systems there is an intrinsic relation between the rupture force distribution and the population of the free-energy well of the bound state, the situation is slightly more complex if reversible systems are considered. For a two-state model, a 'stationary' rupture force distribution that is proportional to the population can be defined and allows to consistently discuss quantities averaged over the transient fluctuations. While irreversible systems are best analyzed in the soft spring limit of small pulling device stiffness and large loading rates, here I argue to use the stiffness of the pulling device as a control parameter in addition to the loading rate.

cond-mat.stat-mech↗

arXiv2012

Higher-order correlation functions and nonlinear response functions in a Gaussian trap model

The four-time correlation function of a general dynamical variable obeying Gaussian statistics is calculated for the trap model with a Gaussian density of states. It is argued that for energy-independent variables this function is reminiscent of the four-time functions that have been discussed earlier in the interpretation of the results of four-dimensional NMR experiments on supercooled liquids. Using an approximative relation between the four-time correlation function and the cubic response function the nonlinear susceptibility is calculated and the results are compared with the corresponding ones resulting from an exact calculation. It is found that the results of the approximation change the qualitative behavior of the modulus of the susceptibility. Whereas in the exact calculation a peak is found in the modulus in most cases, depending on temperature and the additional model parameters no such peak occurs in the approximation. This difference has its origin mainly in an incorrect estimate of the static response. The results are discussed in relation to recent experimental findings.

cond-mat.stat-mech↗

arXiv2012

Nonlinear response theory for Markov processes: Simple models for glassy relaxation

The theory of nonlinear response for Markov processes obeying a master equation is formulated in terms of time-dependent perturbation theory for the Green's functions and general expressions for the response functions up to third order in the external field are given. The nonlinear response is calculated for a model of dipole reorientations in an asymmetric double well potential, a standard model in the field of dielectric spectroscopy. The static nonlinear response is finite with the exception of a certain temperature $T_0$ determined by the value of the asymmetry. In a narrow temperature range around $T_0$, the modulus of the frequency-dependent cubic response shows a peak at a frequency on the order of the relaxation rate and it vanishes for both, low frequencies and high frequencies. At temperatures at which the static response is finite (lower and higher than $T_0$), the modulus is found to decay monotonously from the static limit to zero at high frequencies. In addition, results of calculations for a trap model with a Gaussian density of states are presented. In this case, the cubic response depends on the specific dynamical variable considered and also on the way the external field is coupled to the kinetics of the model. In particular, a set of different dynamical variables is considered that gives rise to identical shapes of the linear susceptibility and only to different temperature dependencies of the relaxation times. It is found that the frequency dependence of the nonlinear response functions, however, strongly depends on the particular choice of the variables. The results are discussed in the context of recent theoretical and experimental findings regarding the nonlinear response of supercooled liquids and glasses.

cond-mat.soft↗

arXiv2011

Memory effects in the relaxation of the Gaussian trap model

We investigate the memory effect in a simple model for glassy relaxation, a trap model with a Gaussian density of states. In this model thermal equilibrium is reached at all finite temperatures and therefore we can consider jumps from low to high temperatures in addition to the quenches usually considered in aging studies. We show that the evolution of the energy following the Kovacs-protocol can approximately be expressed as a difference of two monotonously decaying functions and thus show the existence of a so-called Kovacs hump whenever these functions are not single exponentials. It is well established that the Kovacs effect also occurs in the linear response regime and we show that most of the gross features do not change dramatically when large temperature jumps are considered. However, there is one distinguishing feature that only exists beyond the linear regime which we discuss in detail. For the memory experiment with 'inverted' temperatures, i.e. jumping up and then down again, we find a very similar behavior apart from an opposite sign of the hump.

cond-mat.soft↗

arXiv2010

Statistics of reversible bond dynamics observed in force-clamp spectroscopy

We present a detailed analysis of two-state trajectories obtained from force-clamp spectroscopy (FCS) of reversibly bonded systems. FCS offers the unique possibility to vary the equilibrium constant in two-state kinetics, for instance the unfolding and refolding of biomolecules, over many orders of magnitude due to the force dependency of the respective rates. We discuss two different kinds of counting statistics, the event-counting usually employed in the statistical analysis of two-state kinetics and additionally the so-called cycle-counting. While in the former case all transitions are counted, cycle-counting means that we focus on one type of transitions. This might be advantageous in particular if the equilibrium constant is much larger or much smaller than unity because in these situations the temporal resolution of the experimental setup might not allow to capture all transitions of an event-counting analysis. We discuss how an analysis of FCS data for complex systems exhibiting dynamic disorder might be performed yielding information about the detailed force-dependence of the transition rates and about the time scale of the dynamic disorder. In addition, the question as to which extent the kinetic scheme can be viewed as a Markovian two-state model is discussed.

cond-mat.soft↗

arXiv2010

Aging effects manifested in the potential energy landscape of a model glass former

We present molecular dynamics simulations of a model glass-forming liquid (the binary Kob-Anderson Lennard-Jones model) and consider the distributions of inherent energies and metabasins during aging. In addition to the typical protocol of performing a temperature jump from a high temperature to a low destination temperature, we consider the temporal evolution of the distributions after an 'up-jump', i.e. from a low to a high temperature. In this case the distribution of megabasin energies exhibits a transient two-peak structure. Our results can qualitatively be rationalized in terms of a trap model with a Gaussian distribution of trap energies. The analysis is performed for different system sizes. A detailed comparison with the trap model is possible only for a small system because of major averging effects for larger systems.

cond-mat.dis-nn↗

arXiv2008

Force-clamp spectroscopy of reversible bond breakage

We consider reversible breaking of adhesion bonds or folding of proteins under the influence of a constant external force. We discuss the stochastic properties of the unbinding/rebinding events and analyze their mean number and their variance in the framework of simple two-state models. In the calculations, we exploit the analogy to single molecule fluorescence and particularly between unbinding/rebinding and photon emission events. Environmental fluctuation models are used to describe deviations from Markovian behavior. The second moment of the event-number distribution is found to be very sensitive to possible exchange processes and can thus be used to identify temporal fluctuations of the transition rates.

cond-mat.soft↗

arXiv2008

Dynamic force spectroscopy: analysis of reversible bond-breaking dynamics

The problem of diffusive bond-dissociation in a double well potential under application of an external force is scrutinized. We compute the probability distribution of rupture forces and present a detailed discussion of the influence of finite rebinding probabilities on the dynamic force spectrum. In particular, we focus on barrier crossing upon extension, i.e. under linearly increased load, and upon relaxation starting from completely separated bonds. For large loading rates the rupture force and the rejoining force depend on the loading rate in the expected manner determined by the shape of the potential. For small loading rates the mean forces obtained from pull and relax modes approach each other as the system reaches equilibrium. We investigate the dependence of the rupture force distributions and mean rupture forces on external parameters like cantilever stiffness and influence of a soft linker. We find that depending on the implementation of a soft linker the equilibrium rupture force is either unaffected by the presence of the linker or changes in a predictable way with the linker-compliance. Additionally, we show that it is possible to extract the equilibrium constant of the on- and off-rates from the determination of the equilibrium rupture forces.

cond-mat.soft↗

arXiv2006

Out-of-equilibrium dynamics in a gaussian trap model

The violations of the fluctuation-dissipation theorem are analyzed for a trap model with a gausssian density of states. In this model, the system reaches thermal equilibrium for long times after a quench to any finite temperature and therefore all aging effect are of a transient nature. For not too long times after the quench it is found that the so-called fluctuation-dissipation ratio tends to a non-trivial limit, thus inicating the possibility for the definition of a time scale dependent effective temperature. However, different definitions of the effective temperature yield distinct results. In particular plots of the integrated response versus the correlation function strongly depend on the way they are constructed. Also the definition of effective temperatures in the frequency domain is not unique for the model considered. This may have some implications for the interpretation of results from computer simulations and experimental determinations of effective temperatures.

cond-mat.soft↗

arXiv2006

Aging effects in simple models for glassy relaxation

Aging effects in the two-time correlation function and the response function after a quench from a high temperature to some low temperature are considered for a simple kinetic random energy model exhibiting stretched exponential relaxation. Because the system reaches thermal equilibrium for long times after the quench, all aging effect are of a transient nature. In particular, the violations of the fluctuation-dissipation theorem are considered and it is found that the relation between the response and the two-time correlation function depends on another function, the so-called asymmetry. This asymmetry vanishes in equilibrium but cannot be neglected in the aging regime. It is found that plots of the integrated response versus the correlation function are not applicable to quantify the violations of the fluctuation-dissipation theorem in this particular model. This fact has its origin in the absence of a scaling form of the correlation.

cond-mat.soft↗