Time versus temperature rescaling for coarse grain molecular dynamics simulations

Resolving the dynamic properties of entangled linear polymers in non-equilibrium coarse grain simulation with a priori scaling factors

The molecular weight of polymers can influence the material properties, but the molecular weight at the experiment level sometimes can be a huge burden for property prediction with full-atomic simulations. The traditional bottom-up coarse grain (CG) simulation can reduce the computation cost. However, the dynamic properties predicted by the CG simulation can deviate from the full-atomic simulation result. Usually, in CG simulations, the diffusion is faster and the viscosity and modulus are much lower. The fast dynamics in CG are usually solved by a posteriori scaling on time, temperature, or potential modifications, which usually have poor transferability to other non-fitted physical properties because of a lack of fundamental physics. In this work, a priori scaling factors were calculated by the loss of degrees of freedom and implemented in the iterative Boltzmann inversion. According to the simulation results on 3 different CG levels at different temperatures and loading rates, such a priori scaling factors can help in reproducing some dynamic properties of polycaprolactone in CG simulation more accurately, such as heat capacity, Young's modulus, and viscosity, while maintaining the accuracy in the structural distribution prediction. The transferability of entropy-enthalpy compensation and a dissipative particle dynamics thermostat is also presented for comparison. The proposed method reveals the huge potential for developing customized CG thermostats and offers a simple way to rebuild multiphysics CG models for polymers with good transferability.

Orientation of motion of a flat folding nano-swimmer in soft matter

It is well established that anisotropic molecules do have a preferential direction of motion at short time scales that is washed out at larger times by Brownian noise. Anisotropic molecular motors are able to move at lower temperatures when Brownian noise is smaller suggesting the possibility of oriented motion for larger time scales. We use molecular dynamics simulations to investigate that possibility, calculating the displacements of a simple flat folding molecular nano-swimmer embedded in soft matter. We find actually that the motor displacement is oriented in the direction of its length. We note that the observed orientation of the displacement explains the experimental polarization effect in surface relief gratings formation in agreement with the caterpillar model for azobenzene SRG formation mechanism. That result also suggests a simple route for the creation of molecular motors with oriented displacements.

Recent Progress towards Chemically-Specific Coarse-Grained Simulation Models with Consistent Dynamical Properties

Coarse-grained (CG) models can provide computationally efficient and conceptually simple characterizations of soft matter systems. While generic models probe the underlying physics governing an entire family of free-energy landscapes, bottom-up CG models are systematically constructed from a higher-resolution model to retain a high level of chemical specificity. The removal of degrees of freedom from the system modifies the relationship between the relative time scales of distinct dynamical processes through both a loss of friction and a “smoothing” of the free-energy landscape. While these effects typically result in faster dynamics, decreasing the computational expense of the model, they also obscure the connection to the true dynamics of the system. The lack of consistent dynamics is a serious limitation for CG models, which not only prevents quantitatively accurate predictions of dynamical observables but can also lead to qualitatively incorrect descriptions of the characteristic dynamical processes. With many methods available for optimizing the structural and thermodynamic properties of chemically-specific CG models, recent years have seen a stark increase in investigations addressing the accurate description of dynamical properties generated from CG simulations. In this review, we present an overview of these efforts, ranging from bottom-up parameterizations of generalized Langevin equations to refinements of the CG force field based on a Markov state modeling framework. We aim to make connections between seemingly disparate approaches, while laying out some of the major challenges as well as potential directions for future efforts.

Breakdown of the scallop theorem for an asymmetrical folding molecular motor in soft matter

We use molecular dynamic simulations to investigate the motion of a folding molecular motor inside soft matter. Purcell's scallop theorem forbids the displacement of the motor due to time symmetrical hydrodynamic laws at low Reynolds numbers whatever the asymmetry of the folding and unfolding rates. However, the fluctuation theorems imply a violation of the time symmetry of the motor's trajectories due to the entropy generated by the motor, suggesting a breakdown of the scallop theorem at the nanoscale. To clarify this picture, we study the predicted violation of time reversibility of the motor's trajectories, using two reverse asymmetric folding mechanisms. We actually observe this violation of time reversibility of the motor's trajectories. We also observe the previously reported fluidization of the medium induced by the motor's folding, but find that this induced diffusion is not enough to explain the increase of the motor's displacement. As a result, the motor is not carried by the medium in our system but moves by its own, in violation of the scallop theorem. The observed violation of the scallop theorem opens a route to create very simple molecular motors moving in soft matter environments.

Temperature dependence of the violation of Purcell's theorem experienced by a folding molecular motor

We investigate the violation of Purcell's scallop theorem experienced by a mono-molecular motor, successively folding and unfolding inside a soft matter environment due to an external stimulus. We find a breakdown of the Purcell theorem due to fluctuations, that permits the molecular motor's efficient motion. The diffusion of the motor, its efficiency and its elementary displacement strongly depend on the characteristic time of the folding, but only slightly on the temperature. The increase of the motor's efficiency when the folding characteristic time τ decreases agrees with the fluctuation theorem expectation as the entropy generated inside the medium increases. The constant efficiency with respect to temperature is more difficult to understand as it suggests a generated entropy independent of temperature. In contrast with these results, the diffusion of the medium induced by the motor's folding strongly depends on the temperature, but doesn't depend on the characteristic time of the folding. That result suggests that the medium's diffusion is not due to the motor's displacement. We find that cooperative motions known as dynamic heterogeneity depend significantly on both temperature and folding time, leading in some conditions to a decoupling between dynamic heterogeneity and the medium's diffusion. Eventually, we find that the cooperative motions induced by the folding are larger when the motor cannot move.

Optimizing the motion of a folding molecular motor in soft matter

We use molecular dynamics simulations to investigate the displacement of a periodically folding molecular motor in a viscous environment. Our aim is to find significant parameters to optimize the displacement of the motor. We find that the choice of a massy host or of small host molecules significantly increase the motor displacements. While in the same environment, the motor moves with hopping solid-like motions while the host moves with diffusive liquid-like motions, a result that originates from the motor's larger size. Due to hopping motions, there are thresholds on the force necessary for the motor to reach stable positions in the medium. These force thresholds result in a threshold in the size of the motor to induce a significant displacement, that is followed by plateaus in the motor displacement.

Folding time dependence of the motions of a molecular motor in an amorphous medium

We investigate the dependence of the displacements of a molecular motor embedded inside a glassy material on its folding characteristic time τ_{f}. We observe two different time regimes. For slow foldings (regime I) the diffusion evolves very slowly with τ_{f}, while for rapid foldings (regime II) the diffusion increases strongly with τ_{f}(D≈τ_{f}^{-2}), suggesting two different physical mechanisms. We find that in regime I the motor's displacement during the folding process is counteracted by a reverse displacement during the unfolding, while in regime II this counteraction is much weaker. We notice that regime I behavior is reminiscent of the scallop theorem that holds for larger motors in a continuous medium. We find that the difference in the efficiency of the motor's motion explains most of the observed difference between the two regimes. For fast foldings the motor trajectories differ significantly from the opposite trajectories induced by the following unfolding process, resulting in a more efficient global motion than for slow foldings. This result agrees with the fluctuation theorems expectation for time reversal mechanisms. In agreement with the fluctuation theorems we find that the motors are unexpectedly more efficient when they are generating more entropy, a result that can be used to increase dramatically the motor's motion.

Enhanced diffusion in finite-size simulations of a fragile diatomic glass former

Using molecular dynamics simulations we investigate the finite-size dependence of the dynamical properties of a diatomic supercooled liquid. The simplicity of the molecule permits us to access the microsecond time scale. We find that the relaxation time decreases simultaneously with the strength of cooperative motions when the size of the system decreases. While the decrease of the cooperative motions is in agreement with previous studies, the decrease of the relaxation time opposes what has been reported to date in monatomic glass formers and in silica. This result suggests the presence of different competing physical mechanisms in the relaxation process. For very small box sizes the relaxation times behavior reverses itself and increases strongly when the box size decreases, thus leading to a nonmonotonic behavior. This result is in qualitative agreement with defect and facilitation theories.

How does the motion of the surrounding molecules depend on the shape of a folding molecular motor?

A simplified model of the DR1 molecule is used to realize a systematic study of the surrounding molecules motions dependence on the motor's length and width.

Balancing bond, nonbond, and gō-like terms in coarse grain simulations of conformational dynamics

Characterization of the protein conformational landscape remains a challenging problem, whether it concerns elucidating folding mechanisms, predicting native structures or modeling functional transitions. Coarse-grained molecular dynamics simulation methods enable exhaustive sampling of the energetic landscape at resolutions of biological interest. The general utility of structure-based models is reviewed along with their differing levels of approximation. Simple Gō models incorporate attractive native interactions and repulsive nonnative contacts, resulting in an ideal smooth landscape. Non-Gō coarse-grained models reduce the parameter set as needed but do not include bias to any desired native structure. While non-Gō models have achieved limited success in protein coarse-graining, they can be combined with native structured-based potentials to create a balanced and powerful force field. Recent applications of such Gō-like models have yielded insight into complex folding mechanisms and conformational transitions in large macromolecules. The accuracy and usefulness of reduced representations are also revealed to be a function of the mathematical treatment of the intrinsic bonded topology.

Induced cooperative motions in a medium driven at the nanoscale: searching for an optimum excitation period

Recent results have shown the appearance of induced cooperative motions called dynamic heterogeneity during the isomerization of diluted azobenzene molecules in a host glass-former. In this paper, we raise the issue of the coupling between these "artificial" heterogeneities and the isomerization period. How do these induced heterogeneities differ in the saturation regime and in the linear response regime? Is there a maximum of the heterogeneous motion versus the isomerization rate, and why? Is the heterogeneity evolution with the isomerization rate connected with the diffusion or relaxation time evolution? We use out-of-equilibrium molecular dynamics simulations to answer these questions. We find that the heterogeneity increases in the linear response regime for large isomerization periods and small perturbations. In contrast, the heterogeneity decreases in the saturation regime, i.e., when the isomerization half-period (τp/2) is smaller than the relaxation time of the material (τα). This result enables a test of the effect of cooperative motions on the dynamics using the chromophores as Maxwell demons that destroy or stimulate the cooperative motions. Because the heterogeneities increase in the linear regime and then decrease in the saturation regime, we find a maximum for τp/2≈τα. The induced excitation concentration follows a power-law evolution versus the isomerization rate and then saturates. As a consequence, the α relaxation time is related to the excitation concentration with a power law, a result in qualitative agreement with recent findings in constrained models. This result supports a common origin for the heterogeneities with constrained models and a similar relation to the excitation concentration.