arXiv subjects

Eric Vanden-Eijnden

Publications and source records attributed to Eric Vanden-Eijnden.

108 records · Page 6Linked to original sources

arXiv2012

Force-clamp experiments reveal the free energy profile and diffusion coefficient of the collapse of proteins

We present force-clamp data on the collapse of ubiquitin polyproteins in response to a quench in the force. These nonequilibrium trajectories are analyzed using a general method based on a diffusive assumption of the end-to-end length to reconstruct a downhill free energy profile at 5pN and an energy plateau at 10pN with a slow diffusion coefficient on the order of~100nm^2/s. The shape of the free energy and its linear scaling with the protein length give validity to a physical model for the collapse. However, the length independent diffusion coefficient suggests that internal rather than viscous friction dominates and thermal noise is needed to capture the variability in the measured times to collapse.

physics.bio-ph↗

arXiv2012

A granocentric model captures the statistical properties of monodisperse random packings

We present a generalization of the granocentric model proposed in [Clusel et al., Nature, 2009, 460, 611615] that is capable of describing the local fluctuations inside not only polydisperse but also monodisperse packings of spheres. This minimal model does not take into account the relative particle positions, yet it captures positional disorder through local stochastic processes sampled by efficient Monte Carlo methods. The disorder is characterized by the distributions of local parameters, such as the number of neighbors and contacts, filled solid angle around a central particle and the cell volumes. The model predictions are in good agreement with our experimental data on monodisperse random close packings of PMMA particles. Moreover, the model can be used to predict the distributions of local fluctuations in any packing, as long as the average number of neighbors, contacts and the packing fraction are known. These distributions give a microscopic foundation to the statistical mechanics framework for jammed matter and allow us to calculate thermodynamic quantities such as the compactivity in the phase space of possible jammed configurations.

physics.bio-ph↗

arXiv2010

A patch that imparts unconditional stability to certain explicit integrators for SDEs

This paper proposes a simple strategy to simulate stochastic differential equations (SDE) arising in constant temperature molecular dynamics. The main idea is to patch an explicit integrator with Metropolis accept or reject steps. The resulting `Metropolized integrator' preserves the SDE's equilibrium distribution and is pathwise accurate on finite time intervals. As a corollary the integrator can be used to estimate finite-time dynamical properties along an infinitely long solution. The paper explains how to implement the patch (even in the presence of multiple-time-stepsizes and holonomic constraints), how it scales with system size, and how much overhead it requires. We test the integrator on a Lennard-Jones cluster of particles and `dumbbells' at constant temperature.

math.NA↗

arXiv2010

Non-asymptotic mixing of the MALA algorithm

The Metropolis-Adjusted Langevin Algorithm (MALA), originally introduced to sample exactly the invariant measure of certain stochastic differential equations (SDE) on infinitely long time intervals, can also be used to approximate pathwise the solution of these SDEs on finite time intervals. However, when applied to an SDE with a nonglobally Lipschitz drift coefficient, the algorithm may not have a spectral gap even when the SDE does. This paper reconciles MALA's lack of a spectral gap with its ergodicity to the invariant measure of the SDE and finite time accuracy. In particular, the paper shows that its convergence to equilibrium happens at exponential rate up to terms exponentially small in time-stepsize. This quantification relies on MALA's ability to exactly preserve the SDE's invariant measure and accurately represent the SDE's transition probability on finite time intervals.

math.PR↗

arXiv2010

Stability of 2pi domain walls in ferromagnetic nanorings

The stability of 2pi domain walls in ferromagnetic nanorings is investigated via calculation of the minimum energy path that separates a 2pi domain wall from the vortex state of a ferromagnetic nanoring. Trapped domains are stable when they exist between certain types of transverse domain walls, i.e., walls in which the edge defects on the same side of the magnetic strip have equal sign and thus repel. Here the energy barriers between these configurations and vortex magnetization states are obtained using the string method. Due to the geometry of a ring, two types of 2pi walls must be distinguished that differ by their overall topological index and exchange energy. The minimum energy path corresponds to the expulsion of a vortex. The energy barrier for annihilation of a 2pi wall is compared to the activation energy for transitions between the two ring vortex states.

cond-mat.mes-hall↗

arXiv2009

Pathwise Accuracy and Ergodicity of Metropolized Integrators for SDEs

Metropolized integrators for ergodic stochastic differential equations (SDE) are proposed which (i) are ergodic with respect to the (known) equilibrium distribution of the SDE and (ii) approximate pathwise the solutions of the SDE on finite time intervals. Both these properties are demonstrated in the paper and precise strong error estimates are obtained. It is also shown that the Metropolized integrator retains these properties even in situations where the drift in the SDE is nonglobally Lipschitz, and vanilla explicit integrators for SDEs typically become unstable and fail to be ergodic.

math.NA↗

arXiv2009

Exact rate calculations by trajectory parallelization and twisting

A sampling procedure to compute exactly the rate of activated processes arising in systems at equilibrium or nonequilibrium steady state is presented. The procedure is a generalization of the method in [A. Warmflash, P. Bhimalapuram, and A. R. Dinner, J. Chem. Phys., 127, 154112 (2007); A. Dickson, A. Warmflash, and A. R. Dinner, J. Chem. Phys., 130, 074104 (2009)] in which one performs simulations restricted into cells by using a reinjection rule at the boundaries of the cells which is consistent with the exact probability fluxes through these boundaries. Our generalization uses results from transition path theory which indicate how to twist the dynamics to calculate reaction rates.

physics.comp-ph↗

arXiv2008

Some Critical Issues for the "Equation-Free" Approach to Multiscale Modeling

The "equation-free'' approach has been proposed in recent years as a general framework for developing multiscale methods to efficiently capture the macroscale behavior of a system using only the microscale models. In this paper, we take a close look at some of the algorithms proposed under the "equation-free'' umbrella, the projective integrators and the patch dynamics. We discuss some very simple examples in the context of the "equation-free'' approach. These examples seem to indicate that while its general philosophy is quite attractive and indeed similar to many other approaches in concurrent multiscale modeling, there are severe limitations to the specific implementation proposed by the equation-free approach.

math.NA↗

arXiv2007

Single-Sweep Methods for Free Energy Calculations

A simple, efficient, and accurate method is proposed to map multi-dimensional free energy landscapes. The method combines the temperature-accelerated molecular dynamics (TAMD) proposed in [Maragliano & Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006)] with a variational reconstruction method using radial-basis functions for the representation of the free energy. TAMD is used to rapidly sweep through the important regions of the free energy landscape and compute the gradient of the free energy locally at points in these regions. The variational method is then used to reconstruct the free energy globally from the mean force at these points. The algorithmic aspects of the single-sweep method are explained in detail, and the method is tested on simple examples, compared to metadynamics, and finally used to compute the free energy of the solvated alanine dipeptide in two and four dihedral angles.

physics.comp-ph↗

arXiv2007

Anomalous Dissipation in a Stochastically Forced Infinite-Dimensional System of Coupled Oscillators

We study a system of stochastically forced infinite-dimensional coupled harmonic oscillators. Although this system formally conserves energy and is not explicitly dissipative, we show that it has a nontrivial invariant probability measure. This phenomenon, which has no finite dimensional equivalent, is due to the appearance of some anomalous dissipation mechanism which transports energy to infinity. This prevents the energy from building up locally and allows the system to converge to the invariant measure. The invariant measure is constructed explicitly and some of its properties are analyzed.

math-ph↗

arXiv2007

Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain

Using computer simulations of over 100,000 atoms, the mechanism for the hydrophobic collapse of an idealized hydrated chain is obtained. This is done by coarse-graining the atomistic water molecule positions over 129,000 collective variables that represent the water density field and then using the string method in these variables to compute the minimum free energy pathway (MFEP) for the collapsing chain. The dynamical relevance of the MFEP (i.e. its coincidence with the mechanism of collapse) is validated a posteriori using conventional molecular dynamics trajectories. Analysis of the MFEP provides atomistic confirmation for the mechanism of hydrophobic collapse proposed by ten Wolde and Chandler. In particular, it is shown that lengthscale-dependent hydrophobic dewetting is the rate-limiting step in the hydrophobic collapse of the considered chain.

cond-mat.stat-mech↗

arXiv2006

Simple Systems with Anomalous Dissipation and Energy Cascade

We analyze a class of linear shell models subject to stochastic forcing in finitely many degrees of freedom. The unforced systems considered formally conserve energy. Despite being formally conservative, we show that these dynamical systems support dissipative solutions (suitably defined) and, as a result, may admit unique (statistical) steady states when the forcing term is nonzero. This claim is demonstrated via the complete characterization of the solutions of the system above for specific choices of the coupling coefficients. The mechanism of anomalous dissipations is shown to arise via a cascade of the energy towards the modes ($a_n$) with higher $n$; this is responsible for solutions with interesting energy spectra, namely $\EE |a_n|^2$ scales as $n^{-α}$ as $n\to\infty$. Here the exponents $α$ depend on the coupling coefficients $c_n$ and $\EE$ denotes expectation with respect to the equilibrium measure. This is reminiscent of the conjectured properties of the solutions of the Navier-Stokes equations in the inviscid limit and their accepted relationship with fully developed turbulence. Hence, these simple models illustrate some of the heuristic ideas that have been advanced to characterize turbulence, similar in that respect to the random passive scalar or random Burgers equation, but even simpler and fully solvable.

math-ph↗

arXiv2005

Non-meanfield deterministic limits in chemical reaction kinetics far from equilibrium

A general mechanism is proposed by which small intrinsic fluctuations in a system far from equilibrium can result in nearly deterministic dynamical behaviors which are markedly distinct from those realized in the meanfield limit. The mechanism is demonstrated for the kinetic Monte-Carlo version of the Schnakenberg reaction where we identified a scaling limit in which the global deterministic bifurcation picture is fundamentally altered by fluctuations. Numerical simulations of the model are found to be in quantitative agreement with theoretical predictions.

q-bio.QM↗

arXiv2003

Noise-driven transition to quasi-deterministic limit cycle dynamics in excitable systems

The effect of small-amplitude noise on excitable systems with large time-scale separation is analyzed. It is found that small random perturbations of the fast excitatory variable result in the onset of a quasi-deterministic limit cycle behavior, absent without noise. The limit cycle is established at a critical value of the amplitude of the noise, and its period is nontrivially determined by the relationship between the noise amplitude and the time scale ratio. It is argued that this effect might provide a mechanism by which the function of biological systems operating in noisy environments can be robustly controlled by the level of the noise.

q-bio.QM↗

arXiv2002

Energy landscapes and rare events

Many problems in physics, material sciences, chemistry and biology can be abstractly formulated as a system that navigates over a complex energy landscape of high or infinite dimensions. Well-known examples include phase transitions of condensed matter, conformational changes of biopolymers, and chemical reactions. The energy landscape typically exhibits multiscale features, giving rise to the multiscale nature of the dynamics. This is one of the main challenges that we face in computational science. In this report, we will review the recent work done by scientists from several disciplines on probing such energy landscapes. Of particular interest is the analysis and computation of transition pathways and transition rates between metastable states. We will then present the string method that has proven to be very effective for some truly complex systems in material science and chemistry.

math.NA↗

arXiv2002

Probing Multi-Scale Energy Landscapes Using the String Method

A novel and powerful method is presented for the study of rare switching events in complex systems with multiscale energy landscapes. The method performs an umbrella sampling of the equilibrium distribution of the system in hyperplanes normal to the effective transition pathway, i.e. the transition pathway of a coarse-grained potential which need not to be known beforehand. Rather the effective transition pathway is determined on the fly in an adaptive way by evolving a smooth curve, called a string, that connects the initial and final regions and feels thermally averaged potential forces. Appropriate averages around the string determine the transition rates. Application to an example of solid-solid transformation of a condensed system is presented.

cond-mat↗

arXiv2002

String Method for the Study of Rare Events

We present a new and efficient method for computing the transition pathways, free energy barriers, and transition rates in complex systems with relatively smooth energy landscapes. The method proceeds by evolving strings, i.e. smooth curves with intrinsic parametrization whose dynamics takes them to the most probable transition path between two metastable regions in the configuration space. Free energy barriers and transition rates can then be determined by standard umbrella sampling technique around the string. Applications to Lennard-Jones cluster rearrangement and thermally induced switching of a magnetic film are presented.

cond-mat↗

arXiv2002

Optimal Paths for Spatially Extended Metastable Systems Driven by Noise

The least action principle is exploited as a simulation tool to find the optimal dynamic path for spatially extended systems driven by a small noise. Applications are presented for thermally activated switching of a spatially-extended bistable system as well as the switching dynamics of magnetic thin films. The issue of nucleation versus propagation is discussed and the scaling for the number of nucleation events as a function of the terminal time and other material parameters is computed.

cond-mat.mtrl-sci↗