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Single-molecule fluorescence resonance energy transfer (FRET) experiments are commonly used to study the dynamics of molecular machines. While in vivo molecular processes often break time-reversal symmetry, the temporal directionality of cyclically operating molecular machines is often not evident from single-molecule FRET trajectories, especially in the most common two-color FRET studies. Solving a more quantitative problem of estimating the energy dissipation/entropy production by a molecular machine from single-molecule data is even more challenging. Here, we present a critical assessment of several practical methods of doing so, including Markov-model-based methods and a model-free approach based on an information-theoretical measure of entropy production that quantifies how (statistically) dissimilar observed photon sequences are from their time reverses. The Markov model approach is computationally feasible and may outperform model free approaches, but its performance strongly depends on how well the assumed model approximates the true microscopic dynamics. Markov models are also not guaranteed to give a lower bound on dissipation. Meanwhile, model-free, information-theoretical methods systematically underestimate entropy production at low photoemission rates, and long memory effects in the photon sequences make these methods demanding computationally. There is no clear winner among the approaches studied here, and all methods deserve to belong to a comprehensive data analysis toolkit. 

Storage, organizing, and decorating are important aspects of home design. Buying commercial items for many of these tasks, this can be costly, and reuse is more sustainable. An alternative is a “home hack,” i.e., a functional assembly constructed from existing household items. However, coming up with such hacks requires combining objects to make a physically valid design, which might be difficult to test if they are large, require nailing or screwing to the wall, or if the designer has mobility limitations. We present a design and visualization system, FabHacks, for cre- ating workable functional assemblies. The system is based on a new solver-aided domain-specific language (S-DSL) called FabHaL. By analyzing existing home hacks shared online, we create a design abstraction for connecting household items using predefined con- nection types. We also provide a UI for designing hack assemblies that fulfill a given specification. FabHacks leverages a physics-based solver that finds the expected physical configuration of an assembly design. Our validation includes a user study with our UI, which shows that users can easily create assemblies and explore a range of designs. 

Many nonequilibrium, active processes are observed at a coarse-grained level, where different microscopic configurations are projected onto the same observable state. Such “lumped” observables display memory, and in many cases, the irreversible character of the underlying microscopic dynamics becomes blurred, e.g., when the projection hides dissipative cycles. As a result, the observations appear less irreversible, and it is very challenging to infer the degree of broken time-reversal symmetry. Here we show, contrary to intuition, that by ignoring parts of the already coarse-grained state space we may—via a process called milestoning—improve entropy-production estimates. We present diverse examples where milestoning systematically renders observations “closer to underlying microscopic dynamics” and thereby improves thermodynamic inference from lumped data assuming a given range of memory, and we hypothesize that this effect is quite general. Moreover, whereas the correct general physical definition of time reversal in the presence of memory remains unknown, we here show by means of physically relevant examples that at least for semi-Markov processes of first and second order, waiting-time contributions arising from adopting a naive Markovian definition of time reversal generally must be discarded. 

Whether single-molecule trajectories, observed experimentally or in molecular simulations, can be described using simple models such as biased diffusion is a subject of considerable debate. Memory effects and anomalous diffusion have been reported in a number of studies, but directly inferring such effects from trajectories, especially given limited temporal and/or spatial resolution, has been a challenge. Recently, we proposed that this can be achieved with information-theoretical analysis of trajectories, which is based on the general observation that non-Markov effects make trajectories more predictable and, thus, more “compressible” by lossless compression algorithms. Toy models where discrete molecular states evolve in time were shown to be amenable to such analysis, but its application to continuous trajectories presents a challenge: the trajectories need to be digitized first, and digitization itself introduces non-Markov effects that depend on the specifics of how trajectories are sampled. Here we develop a milestoning-based method for information-theoretical analysis of continuous trajectories and show its utility in application to Markov and non-Markov models and to trajectories obtained from molecular simulations. 

Single-molecule and single-particle tracking experiments are typically unable to resolve fine details of thermal motion at short timescales where trajectories are continuous. We show that, when a diffusive trajectory [Formula: see text] is sampled at finite time intervals δt, the resulting error in measuring the first passage time to a given domain can exceed the time resolution of the measurement by more than an order of magnitude. Such surprisingly large errors originate from the fact that the trajectory may enter and exit the domain while being unobserved, thereby lengthening the apparent first passage time by an amount that is larger than δt. Such systematic errors are particularly important in single-molecule studies of barrier crossing dynamics. We show that the correct first passage times, as well as other properties of the trajectories such as splitting probabilities, can be recovered via a stochastic algorithm that reintroduces unobserved first passage events probabilistically. 

Physical systems ranging from elastic bodies to kinematic linkages are defined on high-dimensional configuration spaces, yet their typical low-energy configurations are concentrated on much lower-dimensional subspaces. This work addresses the challenge of identifying such subspaces automatically: given as input an energy function for a high-dimensional system, we produce a low-dimensional map whose image parameterizes a diverse yet low-energy submanifold of configurations. The only additional input needed is a single seed configuration for the system to initialize our procedure; no dataset of trajectories is required. We represent subspaces as neural networks that map a low-dimensional latent vector to the full configuration space, and propose a training scheme to fit network parameters to any system of interest. This formulation is effective across a very general range of physical systems; our experiments demonstrate not only nonlinear and very low-dimensional elastic body and cloth subspaces, but also more general systems like colliding rigid bodies and linkages. We briefly explore applications built on this formulation, including manipulation, latent interpolation, and sampling. 

We propose a new model and algorithm to capture the high-definition statics of thin shells via coarse meshes. This model predicts global, fine-scale wrinkling at frequencies much higher than the resolution of the coarse mesh; moreover, it is grounded in the geometric analysis of elasticity, and does not require manual guidance, a corpus of training examples, nor tuning of ad hoc parameters. We first approximate the coarse shape of the shell using tension field theory, in which material forces do not resist compression. We then augment this base mesh with wrinkles, parameterized by an amplitude and phase field that we solve for over the base mesh, which together characterize the geometry of the wrinkles. We validate our approach against both physical experiments and numerical simulations, and we show that our algorithm produces wrinkles qualitatively similar to those predicted by traditional shell solvers requiring orders of magnitude more degrees of freedom. 

Abstract We introduce a new mechanism for self‐actuating deployable structures, based on printing a dense pattern of closely‐spaced plastic ribbons on sheets of pre‐stretched elastic fabric. We leverage two shape‐changing effects that occur when such an assembly is printed and allowed to relax: first, the incompressible plastic ribbons frustrate the contraction of the fabric back to its rest state, forcing residual strain in the fabric and creating intrinsic curvature. Second, the differential compression at the interface between the plastic and fabric layers yields abilayer effectin the direction of the ribbons, making each ribbon buckle into an arc at equilibrium state and creating extrinsic curvature. We describe an inverse design tool to fabricate low‐cost, lightweight prototypes of freeform surfaces using the controllable directional distortion and curvature offered by this mechanism. The core of our method is a parameterization algorithm that bounds surface distortions along and across principal curvature directions, along with a pattern synthesis algorithm that covers a surface with ribbons to match the target distortions and curvature given by the aforementioned parameterization. We demonstrate the flexibility and accuracy of our method by fabricating and measuring a variety of surfaces, including nearly‐developable surfaces as well as surfaces with positive and negative mean curvature, which we achieve thanks to a simple hardware setup that allows printing on both sides of the fabric.