Related papers: Infinite Switch Simulated Tempering in Force (FISS…
Molecular dynamics simulations have become essential in many areas of atomistic modelling from drug discovery to materials science. They provide critical atomic-level insights into key dynamical events experiments cannot easily capture.…
The simulated tempering (ST) is an important method to deal with systems whose phase spaces are hard to sample ergodically. However, it uses accepting probabilities weights which often demand involving and time consuming calculations. Here…
An integrate-and-fire time-encoding machine (IF-TEM) is an effective asynchronous sampler that translates amplitude information into non-uniform time sequences. In this work, we propose a novel Adaptive IF-TEM (AIF-TEM) approach. This…
Traction Force Microscopy (TFM) is a technique used to determine the tensions that a biological cell conveys to the underlying surface. Typically, TFM requires culturing cells on gels with fluorescent beads, followed by bead displacement…
The remarkable accuracy and versatility of single-molecule techniques make possible new measurements that are not feasible in bulk assays. Among these, the precise estimation of folding free energies using fluctuation theorems in…
A number of problems arise when long-range forces, such as those governed by Bessel functions, are used in particle-particle simulations. If a simple cut-off for the interaction is used, the system may find an equilibrium configuration at…
A family of fast sampling methods is introduced here for molecular simulations of systems having rugged free energy landscapes. The methods represent a generalization of a strategy consisting of adjusting a model for the free energy as a…
We consider here systems with piecewise linear dynamics that are periodically sampled with a given period {\tau} . At each sampling time, the mode of the system, i.e., the parameters of the linear dynamics, can be switched, according to a…
Interest in equilibrium-based sampling methods has grown with recent advances in computational hardware and Markov state modeling (MSM) methods, yet outstanding questions remain that hinder widespread adoption. Namely, how do sampling…
We derive a new class of statistical tests for generalized linear models based on thresholding point estimators. These tests can be employed whether the model includes more parameters than observations or not. For linear models, our tests…
Deformable elastic bodies in viscous and viscoelastic media constitute a large portion of synthetic and biological complex fluids. We present a parallelized 3D-simulation methodology which fully resolves the momentum balance in the solid…
In this paper, we propose a stochastic optimization method that adaptively controls the sample size used in the computation of gradient approximations. Unlike other variance reduction techniques that either require additional storage or the…
The study is devoted to the geometrically nonlinear simulation of fiber-reinforced composite structures. The applicability of the multiplicative approach to the simulation of viscoelastic properties of a composite material is assessed,…
Sampling is a fundamental problem in computer science and statistics. However, for a given task and stream, it is often not possible to choose good sampling probabilities in advance. We derive a general framework for adaptively changing the…
Inferring the input parameters of simulators from observations is a crucial challenge with applications from epidemiology to molecular dynamics. Here we show a simple approach in the regime of sparse data and approximately correct models,…
A novel method combining the ensemble refinement by maximum entropy principle and the force field fitting approach is presented. Its formulation allows to continuously interpolate in between these two methods, which can thus be interpreted…
Objective: This paper presents a force control scheme for brief isotonic holds in an isometrically contracted muscle tissue, with minimal overshoot and settling time to measure its shortening velocity, a key parameter of muscle function.…
Multisite phosphorylation plays an important role in regulating switchlike protein activity and has been used widely in mathematical models. With the development of new experimental techniques and more molecular data, molecular…
We consider the dynamics of a rigid filament in a motor protein assay under external loading. The motor proteins are modeled as active harmonic linkers with tail ends immobilized on a substrate. Their heads attach to the filament…
We present a new method, Non-Stationary Forward Flux Sampling, that allows efficient simulation of rare events in both stationary and non-stationary stochastic systems. The method uses stochastic branching and pruning to achieve uniform…