Based on the trajectories of the separation between water molecule pairs from MD simulations, we investigate the bond breakage dynamics in bulk water. From the spectrum of mean first-passage times, the Fokker-Planck equation allows us to derive the diffusivity profile along the separation coordinate and thus to unambiguously disentangle the effects of free-energy and local friction on the separation kinetics. For tightly coordinated water the friction is six times higher than in bulk, which can be interpreted in terms of a dominant reaction path that involves additional orthogonal coordinates.
We investigate the dynamic heterogeneities of glassy particle systems in the theoretical schemes of bond breakage and four-point correlation functions. In the bond-breakage scheme, we introduce the structure factor S_b(q,t) and the susceptibility chi_b(t) to detect the spatial correlations of configuration changes. Here chi_b(t) attains a maximum at t =t_b^max as a function of time t, where the fraction of the particles with broken bonds phi_b(t)$ is about 1/2. In the four-point scheme, treating the structure factor S_4(q,t) and the susceptibility chi_4(t), we detect superpositions of the hete…
We investigate the fragmentation dynamics of an atomic chain under tensile stress. We have classified the location, stability type (indices) and energy of all equilibria for the general $n$-particle chain, and have highlighted the importance of saddle points with index $> 1$. We show that for an $n=2$-particle chain under tensile stress the index 2 saddle plays a central role in organizing the dynamics. We apply normal form theory to analyze phase space structure and dynamics in a neighborhood of the index 2 saddle. We define a phase dividing surface (DS) that enables us to classify trajectori…
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 se…
We consider the thermal breakage of a tethered polymer chain of discrete segments coupled by Morse potentials under constant tensile stress. The chain dynamics at the onset of fracture is studied analytically by Kramers-Langer multidimensional theory and by extensive Molecular Dynamics simulations in 1D- and 3D-space. Comparison with simulation data in one- and three dimensions demonstrates that the Kramers-Langer theory provides good qualitative description of the process of bond-scission as caused by a {\em collective} unstable mode. We derive distributions of the probability for scission ov…
Supercooled water exhibits remarkably slow dynamics similar to the behavior observed for various glass-forming liquids. The local order of tetrahedral structures due to hydrogen-bonds (H-bonds) increases with decreasing temperature. Thus, it is important to clarify the temperature dependence of the H-bond breakage process. This was investigated here using molecular dynamics simulations of TIP4P supercooled water. The two-dimensional (2D) potential of mean force (PMF) is presented using combinations of intermolecular distance and angle between two water molecules. The saddle point of the 2D PMF…
Sacrificial bonds and hidden length in structural molecules account for the greatly increased fracture toughness of biological materials compared to synthetic materials without such structural features, by providing a molecular-scale mechanism for energy dissipation. One example is in the polymeric glue connection between collagen fibrils in animal bone. In this paper, we propose a simple kinetic model that describes the breakage of sacrificial bonds and the release of hidden length, based on Bell's theory. We postulate a master equation governing the rates of bond breakage and formation. This…
We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion between bond types. Bond formation can be controlled to limit the maximal functionality of a bead with respect to various bond types. Concomitant with the bond dynamics, angular and dihedral interactions are dynamically introduced between newly connected triplets and quartets of beads, where the interaction type is determined from the local pattern of bead an…
The breakage of a polymer chain of segments, coupled by anharmonic bonds with applied constant external tensile force is studied by means of Molecular Dynamics simulation. We show that the mean life time of the chain becomes progressively independent of the number of bonds as the pulling force grows. The latter affects also the rupture rates of individual bonds along the polymer backbone manifesting the essential role of inertial effects in the fragmentation process. The role of local defects, temperature and friction in the scission kinetics is also examined.
We present a modified model based on shear rate and aging time dependent static friction between a soft solid such as gelatin hydrogel and a hard surface for instance glass surface. Earlier the model for static friction (Juvekar and Singh, 2016) considered only the bond rupture process as a result, the friction model over predicts the static friction in the experiment. The friction model now takes into account both formation and rupture of molecular chains at the sliding interface. It is also assumed that age of the newly formed bonds during the rupture process is the same as the aging time. A…
We study a highly supercooled two-dimensional fluid mixture via molecular dynamics simulation. We follow bond breakage events among particle pairs, which occur on the scale of the $α$ relaxation time $τ_α$. Large scale heterogeneities analogous to the critical fluctuations in Ising systems are found in the spatial distribution of bonds which are broken in a time interval with a width of order $0.05τ_α$. The structure factor of the broken bond density is well approximated by the Ornstein-Zernike form. The correlation length is of order $100 σ_1$ at the lowest temperature studied, $σ_1$ being th…
The shear-jamming of dense suspensions can be strongly affected by molecular-scale interactions between particles, e.g. by chemically controlling their propensity for hydrogen bonding. However, hydrogen bonding not only enhances interparticle friction, a critical parameter for shear jamming, but also introduces (reversible) adhesion, whose interplay with friction in shear-jamming systems has so far remained unclear. Here, we present atomic force microscopy studies to assess interparticle adhesion, its relationship to friction, and how these attributes are influenced by urea, a molecule that in…
Yielding behavior is well known in attractive colloidal suspensions. Adhesive non-Brownian suspensions, in which the interparticle bonds are due to finite-size contacts, also show yielding behavior. We use a combination of steady-state, oscillatory and shear-reversal rheology to probe the physical origins of yielding in the latter class of materials, and find that yielding is not simply a matter of breaking adhesive bonds, but involves unjamming from a shear-jammed state in which the micro-structure has adapted to the direction of the applied load. Comparison with a recent constraint-based rhe…
Cooperative binding affects many processes in biology, but it is commonly addressed only in equilibrium. In this work we explore dynamical cooperativity in driven systems, where the cooperation occurs because some of the bonds change the dynamical response of the system to a regime where the other bonds become active. To investigate such cooperativity we study the frictional binding between two flow driven surfaces that interact through a large population of activated bonds. In particular, we study systems where each bond can have two different modes: one mode corresponds to a fast forming yet…
The thermal degradation of a graphene-like two-dimensional triangular membrane with bonds undergoing temperature-induced scission is studied by means of Molecular Dynamics simulation using Langevin thermostat. We demonstrate that the probability distribution of breaking bonds is highly peaked at the rim of the membrane sheet at lower temperature whereas at higher temperature bonds break at random anywhere in the hexagonal flake. The mean breakage time $τ$ is found to decrease with the total number of network nodes $N$ by a power law $τ\propto N^{-0.5}$ and reveals an Arrhenian dependence on te…
We present an experimental investigation of the non stationary frictional properties of multicontact interfaces between rough elastomers and rough hard glass at low velocities (<= 200 mu m s^{-1}). These systems, for which the deformation contribution to friction is negligible, are shown to exhibit a phenomenology which is similar to what is observed for non elastomeric materials in the same multi-contact configuration, and which are quantitatively described by the state- and rate-dependent friction laws. This permits to identify clearly the two contributions to adhesive friction which are mix…
In this article, we present a mathematical model that answers a classical question concerning how much force, which is generally called static friction force, will it require to initiate the motion of a soft solid block such as gel, rubber or elastomer on a hard surface for instance glass surface. The model uses population balance of the bonds between the polymer chains of the soft solid and the hard surface to estimate rate and aging time dependent static friction. The model predicts that under certain range of the pulling velocity, the friction stress at the onset of sliding (static friction…
We consider the fracture of a free-standing two-dimensional (2D) elastic-brittle network to be used as protective coating subject to constant tensile stress applied on its rim. Using a Molecular Dynamics simulation with Langevin thermostat, we investigate the scission and recombination of bonds, and the formation of cracks in the 2D graphene-like hexagonal sheet for different pulling force $f$ and temperature $T$. We find that bond rupture occurs almost always at the sheet periphery and the First Mean Breakage Time $<τ>$ of bonds decays with membrane size as $<τ> \propto N^{-β}$ where $β\appro…
A decade ago, Budakian and Putterman (Phys. Rev. Lett., {\bf 85}, 1000 (2000)) ascribed friction to the formation of bonds arising from contact charging when a gold tip of a surface force apparatus was dragged on polymethylmethacrylate surface. We propose a stick-slip model that captures the observed correlation between stick-slip events and charge transfer, and the lack of dependence of the scale factor connecting the force jumps and charge transfer on normal load. Here, stick-slip dynamics arises as a competition between the visco-elastic and plastic deformation time scales and that due to t…
A computationally-efficient method for evaluating friction in molecular rotary bearings is presented. This method estimates drag from fluctuations in molecular dynamics simulations via the fluctuation-dissipation theorem. This is effective even for simulation times short compared to a bearing's energy damping time and for rotation speeds comparable to or below typical thermal values. We apply this method to two molecular rotary bearings of similar size at 300K: previously studied nested (9,9)/(14,14) double-walled carbon nanotubes and a hypothetical rotary joint consisting of single acetylenic…
Highly supercooled liquids with soft-core potentials are studied via molecular dynamics simulations in two and three dimensions in quiescent and sheared conditions.We may define bonds between neighboring particle pairs unambiguously owing to the sharpness of the first peak of the pair correlation functions. Upon structural rearrangements, they break collectively in the form of clusters whose sizes grow with lowering the temperature $T$. The bond life time $τ_b$, which depends on $T$ and the shear rate $\gdot$, is on the order of the usual structural or $α$ relaxation time $τ_α$ in weak shear $…
The violation of Stokes--Einstein (SE) relation $D\sim (η/T)^{-1}$ between the shear viscosity $η$ and the translational diffusion constant $D$ at temperature $T$ is of great importance for characterizing anomalous dynamics of supercooled water. Determining which time scales play key roles in the SE violation remains elusive without the measurement of $η$. Here we provide comprehensive simulation results of the dynamic properties involving $η$ and $D$ in TIP4P/2005 supercooled water. This enabled the thorough identification of the appropriate time scales for SE relation $Dη/T$. In particular, …
