arXiv subjects

Roland R. Netz

Publications and source records attributed to Roland R. Netz.

At least 73 records · Page 4Linked to original sources

arXiv2020

Fluids at the Nanoscale: from continuum to sub-continuum transport

Nanofluidics has firmly established itself as a new field in fluid mechanics, as novel properties have been shown to emerge in fluids at the nanometric scale. Thanks to recent developments in fabrication technology, artificial nanofluidic systems are now being designed at the scale of biological nanopores. This ultimate step in scale reduction has pushed the development of new experimental techniques and new theoretical tools, bridging fluid mechanics, statistical mechanics and condensed matter physics. This review is intended as a toolbox for fluids at the nanometre scale. After presenting the basic equations that govern fluid behaviour in the continuum limit, we will show how these equations break down and new properties emerge in molecular scale confinement.

physics.flu-dyn↗

arXiv2020

Approach to equilibrium and non-equilibrium stationary distributions of interacting many-particle systems that are coupled to different heat baths

A Hamiltonian-based model of many harmonically interacting massive particles that are subject to linear friction and coupled to heat baths at different temperatures is used to study the dynamic approach to equilibrium and non-equilibrium stationary states. Based on the exactly calculated dynamic approach to the stationary distribution, the functional that governs this approach, which is called the free entropy, is constructed. For the stationary distribution the free entropy becomes maximal and its time derivative is minimal and vanishes. Thus, the free entropy characterizes equilibrium as well as non-equilibrium stationary distributions by their extremal and stability properties. For an equilibrium system, i.e. if all heat baths have the same temperature, the free entropy equals the negative free energy divided by temperature. Using a systematic perturbative scheme for calculating velocity and position correlations in the overdamped massless limit, explicit results for few particles are presented: For two particles localization in position and momentum space is demonstrated in the non-equilibrium stationary state, indicative of a tendency to phase separate. For three elastically interacting particles heat flows from a particle coupled to a cold reservoir to a particle coupled to a warm reservoir if the third reservoir is sufficiently hot. Active particle models can be described in the same general framework, which thereby allows to characterize their entropy production not only in the stationary state but also in the approach to the stationary non-equilibrium state. Finally, the connection to non-equilibrium thermodynamics formulations that include the reservoir entropy production is discussed.

cond-mat.stat-mech↗

arXiv2020

Particle Diffusivity and Free-Energy Profiles in Inhomogeneous Hydrogel Systems from Time-Resolved Penetration Profiles

A combined experimental/theoretical method to simultaneously determine diffusivity and free-energy profiles of particles that penetrate into inhomogeneous hydrogel systems is presented. As the only input, arbitrarily normalized concentration profiles from fluorescence intensity data of labeled tracer particles for different penetration times are needed. The method is applied to dextran molecules of varying size which penetrate into hydrogels of polyethylene-glycol (PEG) chains with different lengths that are covalently cross-linked by hyperbranched polyglycerol (hPG) hubs. Extracted dextran bulk diffusivities agree well with fluorescence correlation spectroscopy data obtained separately. Scaling laws for dextran diffusivities and free energies inside the hydrogel are identified as a function of the dextran mass. An elastic free-volume model that includes dextran as well as PEG linker flexibility describes the repulsive dextran-hydrogel interaction free energy, which is of steric origin, quantitatively and furthermore suggests that the hydrogel mesh-size distribution is rather broad and particle penetration is dominated by large hydrogel pores. Particle penetration into hydrogels is for steric particle-hydrogel interactions thus suggested to be governed by an elastic size-filtering mechanism that involves the tail of the hydrogel pore-size distribution.

cond-mat.soft↗

arXiv2020

Viral air load due to sedimenting and evaporating droplets produced by speaking

The effect of evaporation on droplet sedimentation times is crucial for estimating the risk of infection from virus-containing airborne droplets. For droplet radii in the range 100 nm < R < 60 μm, evaporation can be described in the stagnant-flow approximation and is diffusion limited. Analytical equations are presented for the droplet evaporation rate, the time-dependent droplet size and the sedimentation time, including the significant effect of evaporation cooling. Evaporation makes the time for large droplets to sediment much longer and thus significantly increases the viral air load. Using recent estimates for SARS-CoV-2 concentrations in sputum and droplet production rates while speaking, a single infected person that constantly speaks without a mouth cover produces a total air load of more than 10^4 virions. In a mid-size closed room, this leads to a viral inhalation frequency of at least 2.5 per minute. Low relative humidity, as encountered inside buildings in winter and in airliners, speeds evaporation and thus keeps initially larger droplets suspended in air.

cond-mat.soft↗

arXiv2020

A rigorous derivation and energetics of a wave equation with fractional damping

We consider a linear system that consists of a linear wave equation on a horizontal hypersurface and a parabolic equation in the half space below. The model describes longitudinal elastic waves in organic monolayers at the water-air interface, which is an experimental setup that is relevant for understanding wave propagation in biological membranes. We study the scaling regime where the relevant horizontal length scale is much larger than the vertical length scale and provide a rigorous limit leading to a fractionally-damped wave equation for the membrane. We provide the associated existence results via linear semigroup theory and show convergence of the solutions in the scaling limit. Moreover, based on the energy-dissipation structure for the full model, we derive a natural energy and a natural dissipation function for the fractionally-damped wave equation with a time derivative of order 3/2

math.AP↗

arXiv2020

Emergence of molecular friction in liquids: bridging between the atomistic and hydrodynamic pictures

Friction in liquids arises from conservative forces between molecules and atoms. Although the hydrodynamics at the nanoscale is subject of intense research and despite the enormous interest in the non-Markovian dynamics of single molecules and solutes, the onset of friction from the atomistic scale so far could not be demonstrated. Here, we fill this gap based on frequency-resolved friction data from high-precision simulations of three prototypical liquids, including water. Combining with rigorous theoretical arguments, we show that friction in liquids emerges abruptly at a characteristic frequency, beyond which viscous liquids appear as non-dissipative, elastic solids; as a consequence, its origin is non-local in time. Concomitantly, the molecules experience Brownian forces that display persistent correlations and long-lasting memory. A critical test of the generalised Stokes-Einstein relation, mapping the friction of single molecules to the viscoelastic response of the macroscopic sample, disproves the relation for Newtonian fluids, but substantiates it exemplarily for water and a moderately supercooled liquid. The employed approach is suitable to yield novel insights into vitrification mechanisms and the intriguing mechanical properties of soft materials.

cond-mat.stat-mech↗

arXiv2020

Energy Transfer within the Hydrogen Bonding Network of Water Following Resonant Terahertz Excitation

Energy dissipation in water is very fast and more efficient than in many other liquids. This behavior is commonly attributed to the intermolecular interactions associated with hydrogen bonding. Here, we investigate the dynamic energy flow in the hydrogen-bond network of liquid water by a pump-probe experiment. We resonantly excite intermolecular degrees of freedom with ultrashort single-cycle terahertz pulses and monitor its Raman response. By using ultrathin sample-cell windows, a background-free bipolar signal whose tail relaxes mono-exponentially is obtained. The relaxation is attributed to the molecular translational motions, using complementary experiments, force-field and ab initio molecular dynamics simulations. They reveal an initial coupling of the terahertz electric field to the molecular rotational degrees of freedom whose energy is rapidly transferred, within the excitation pulse duration, to the restricted-translational motion of neighboring molecules. This rapid energy transfer may be rationalized by the strong anharmonicity of the intermolecular interactions.

cond-mat.soft↗

arXiv2020

Molecular interpretation of the non-Newtonian viscoelastic behavior of liquid water at high frequencies

Using classical as well as ab-initio molecular dynamics simulations, we calculate the frequency-dependent shear viscosity of pure water and water-glycerol mixtures. In agreement with recent experiments, we find deviations from Newtonian-fluid behavior in the THz regime. Based on an extension of the Maxwell model, we introduce a viscoelastic model to describe the observed viscosity spectrum of pure water. We find four relaxation modes in the spectrum which we attribute to i) hydrogen-bond network topology changes, ii) hydrogen-bond stretch vibrations of water pairs, iii) collective vibrations of water molecule triplets, and iv) librational excitations of individual water molecules. Our model quantitatively describes the viscoelastic response of liquid water on short timescales, where the hydrodynamic description via a Newtonian-fluid model breaks down.

physics.flu-dyn↗

arXiv2020

Exploring the Absorption Spectrum of Simulated Water from MHz to the Infrared

Absorption spectra of liquid water at 300 K are calculated from both classical and density functional theory molecular dynamics simulation data, which together span from 1 MHz to hundreds of THz, agreeing well with experimental data qualitativley and quantitavely over the entire range, including the IR modes, the microwave peak, and the intermediate THz bands. The spectra are decomposed into single-molecular and collective components as well as into components due to molecular reorientations and changes in induced intramolecular dipole moments. These decompositions shed new light on the motions underlying the librational and translational (hydrogen-bond stretch) bands at 20 and 5 THz respectively: interactions between donor protons and acceptor lone pair electrons are shown to be important for the line shape in both librational and translational regimes, and in- and out-of-phase librational dimer modes are observed and explored.

physics.chem-ph↗

arXiv2019

Non-Markovian barrier crossing with two-time-scale memory is dominated by the faster memory component

We investigate non-Markovian barrier-crossing kinetics of a massive particle in one dimension in the presence of a memory function that is the sum of two exponentials with different memory times $τ_1$ and $τ_2$. Our Langevin simulations for the special case where both exponentials contribute equally to the total friction show that the barrier crossing time becomes independent of the longer memory time if at least one of the two memory times is larger than the intrinsic diffusion time. When we associate memory effects with coupled degrees of freedom that are orthogonal to a one-dimensional reaction coordinate, this counterintuitive result shows that the faster orthogonal degrees of freedom dominate barrier-crossing kinetics in the non-Markovian limit and that the slower orthogonal degrees become negligible, quite contrary to the standard time-scale separation assumption and with important consequences for the proper setup of coarse-graining procedures in the non-Markovian case. By asymptotic matching and symmetry arguments, we construct a crossover formula for the barrier crossing time that is valid for general multi-exponential memory kernels. This formula can be used to estimate barrier-crossing times for general memory functions for high friction, i.e. in the overdamped regime, as well as for low friction, i.e. in the inertial regime. Typical examples where our results are important include protein folding in the high-friction limit and chemical reactions such as proton-transfer reactions in the low-friction limit.

physics.chem-ph↗

arXiv2018

Cold denaturation of RNA secondary structures with loop entropy and quenched disorder

We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In addition to the expected melting at high temperature, a cold melting transition appears. Our results suggest that the cold denaturation of RNA found experimentally is, in fact, a continuous phase transition triggered by quenched sequence disorder. We calculate both hot and cold melting critical temperatures for the competing energy scenario between favorable and unfavorable base pairs and present a phase diagram as a function of the loop exponent and temperature.

physics.bio-ph↗

arXiv2017

Nonlinear fractional waves at elastic interfaces

We derive the nonlinear fractional surface wave equation that governs compression waves at an interface that is coupled to a viscous bulk medium. The fractional character of the differential equation comes from the fact that the effective thickness of the bulk layer that is coupled to the interface is frequency dependent. The nonlinearity arises from the nonlinear dependence of the interface compressibility on the local compression, which is obtained from experimental measurements and reflects a phase transition at the interface. Numerical solutions of our nonlinear fractional theory reproduce several experimental key features of surface waves in phospholipid monolayers at the air-water interface without freely adjustable fitting parameters. In particular, the propagation length of the surface wave abruptly increases at a threshold excitation amplitude. The wave velocity is found to be of the order of 40 cm/s both in experiments and theory and slightly increases as a function of the excitation amplitude. Nonlinear acoustic switching effects in membranes are thus shown to arise purely based on intrinsic membrane properties, namely the presence of compressibility nonlinearities that accompany phase transitions at the interface.

physics.flu-dyn↗

arXiv2015

Shear-induced unfolding and enzymatic cleavage of full-length VWF multimers

Proteolysis of the multimeric blood coagulation protein von Willebrand Factor (VWF) by ADAMTS13 is crucial for prevention of microvascular thrombosis. ADAMTS13 cleaves VWF within the mechanosensitive A2 domain, which is believed to open under shear flow. Here, we combine Fluorescence Correlation Spectroscopy (FCS) and a microfluidic shear cell to monitor real-time kinetics of full-length VWF proteolysis as a function of shear stress. For comparison, we also measure the Michaelis-Menten kinetics of ADAMTS13 cleavage of wild-type VWF in the absence of shear but partially denaturing conditions. Under shear, ADAMTS13 activity on full-length VWF arises without denaturing agent as evidenced by FCS and gel-based multimer analysis. In agreement with Brownian hydrodynamics simulations, we find a sigmoidal increase of the enzymatic rate as a function of shear at a threshold shear rate 5522/s. The same flow-rate dependence of ADAMTS13 activity we also observe in blood plasma, which is relevant to predict hemostatic dysfunction.

physics.bio-ph↗

arXiv2015

The mean shape of transition and first-passage paths

We calculate the mean shape of transition paths and first-passage paths based on the one-dimensional Fokker-Planck equation in an arbitrary free energy landscape including a general inhomogeneous diffusivity profile. The transition path ensemble is the collection of all paths that do not revisit the start position $x_A$ and that terminate when first reaching the final position $x_B$. In contrast, a first-passage path can revisit but not cross its start position $x_A$ before it terminates at $x_B$. Our theoretical framework employs the forward and backward Fokker-Planck equations as well as first-passage, passage, last-passage and transition-path time distributions, for which we derive the defining integral equations. We show that the mean time at which the transition path ensemble visits an intermediate position $x$ is equivalent to the mean first-passage time of reaching the starting position $x_A$ from $x$ without ever visiting $x_B$. The mean shape of first-passage paths is related to the mean shape of transition paths by a constant time shift. Since for large barrier height $U$ the mean first-passage time scales exponentially in $U$ while the mean transition path time scales linearly inversely in $U$, the time shift between first-passage and transition path shapes is substantial. We present explicit examples of transition path shapes for linear and harmonic potentials and illustrate our findings by trajectories generated from Brownian dynamics simulations.

physics.bio-ph↗

arXiv2013

Global analysis of the ground-state wrapping conformation of a charged polymer on an oppositely charged nano-sphere

We investigate the wrapping conformations of a strongly adsorbed polymer chain on an oppositely charged nano-sphere by employing a reduced (dimensionless) representation of a primitive chain-sphere model. This enables us to determine the global phase behavior of the chain conformation in a wide range of values for the system parameters including the chain contour length, its linear charge density and persistence length as well as the nano-sphere charge and radius, and also the salt concentration in the bathing solution. The phase behavior of a charged chain-sphere complex can be described in terms of a few distinct conformational symmetry classes (phases) separated by continuous or discontinuous transition lines which are determined by means of appropriately defined (order) parameters. Our results can be applied to a wide class of strongly coupled polymer-sphere complexes including, for instances, complexes that comprise a mechanically flexible or semiflexible polymer chain or an extremely short or long chain and, as a special case, include the previously studied example of DNA-histone complexes.

cond-mat.soft↗

arXiv2013

Elasticity of DNA and the effect of Dendrimer Binding

Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic properties of short double stranded DNA (dsDNA) and the effect of dendrimer binding using fully atomistic molecular dynamics and numerical simulations. In equilibrium at room temperature, the contour length distribution P(L) and end-to-end distance distribution P(R) are nearly Gaussian, the former gives an estimate of the stretch modulus γ_1 of dsDNA in quantitative agreement with the literature value. The bend angle distribution P(θ) of the dsDNA also has a Gaussian form and allows to extract a persistence length, L_p of 43 nm. When the dsDNA is compacted by positively charged dendrimer, the stretch modulus stays invariant but the effective bending rigidity estimated from the end-to-end distance distribution decreases dramatically due to backbone charge neutralization of dsDNA by dendrimer. We support our observations with numerical solutions of the worm-like-chain (WLC) model as well as using non-equilibrium dsDNA stretching simulations. These results are helpful in understanding the dsDNA elasticity at short length scales as well as how the elasticity is modulated when dsDNA binds to a charged object such as a dendrimer or protein.

physics.bio-ph↗

arXiv2012

Hydrodynamic effects in driven soft matter

Recent theoretical works exploring the hydrodynamics of soft material in non-equilibrium situations are reviewed. We discuss the role of hydrodynamic interactions for three different systems: i) the deformation and orientation of sedimenting semiflexible polymers, ii) the propulsion and force-rectification with a nano-machine realized by a rotating elastic rod, and iii) the deformation of a brush made of grafted semiflexible polymers in shear flows. In all these examples deformable polymers are subject to various hydrodynamic flows and hydrodynamic interactions. Perfect stiff nano-cylinders are known to show no orientational effects as they sediment through a viscous fluid, but it is the coupling between elasticity and hydrodynamic torques that leads to an orientation perpendicular to the direction of sedimentation. Likewise, a rotating stiff rod does not lead to a net propulsion in the Stokes limit, but if bending is allowed an effective thrust develops whose strength and direction is independent of the sense of rotation and thus acts as a rectification device. Lastly, surface-anchored polymers are deformed by shear flows, which modifies the effective hydrodynamic boundary condition in a non-linear fashion. All these results are obtained with hydrodynamic Brownian dynamics simulation techniques, as appropriate for dilute systems. Scaling analyses are presented when possible. The common theme is the interaction between elasticity of soft matter and hydrodynamics, which can lead to qualitatively new effects.

cond-mat.soft↗

arXiv2011

Friction contribution to water-bond breakage kinetics

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.

cond-mat.soft↗