Related papers: Single-molecule force spectroscopy: Practical limi…
We analyze the nonlinear Helmholtz oscillator in the presence of fractional damping, a characteristic feature in several physical situations. In our specific scenario, as well as in the non-fractional case, for large enough excitation…
Resistance force exerted on an obstacle in a gravity-driven slow granular silo flow is studied by experiments and numerical simulations. In a two-dimensional granular silo, an obstacle is placed just above the exit. Then, steady discharge…
Wet-lab experiments, in which the dynamics within living cells are observed, are usually costly and time consuming. This is particularly true if single-cell measurements are obtained using experimental techniques such as flow-cytometry or…
The length-scale dependence of the dynamic entropy is studied in a molecular dynamics simulation of a binary Lennard-Jones liquid above the mode-coupling critical temperature $T_c$. A number of methods exist for estimating the entropy of…
High dimensional hypothesis test deals with models in which the number of parameters is significantly larger than the sample size. Existing literature develops a variety of individual tests. Some of them are sensitive to the dense and small…
We consider a fully-connected network of leaky integrate-and-fire neurons with spike-timing-dependent plasticity. The plasticity is controlled by a parameter representing the expected weight of a synapse between neurons that are firing…
The Constraint Satisfaction Problem (CSP) framework offers a simple and sound basis for representing and solving simple decision problems, without uncertainty. This paper is devoted to an extension of the CSP framework enabling us to deal…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
Single-molecule localization microscopy allows practitioners to locate and track labeled molecules in biological systems. When extracting diffusion coefficients from the resulting trajectories, it is common practice to perform a linear fit…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
Molecular dynamics (MD) simulations allow investigating the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields,…
We study efficient importance sampling techniques for particle filtering (PF) when either (a) the observation likelihood (OL) is frequently multimodal or heavy-tailed, or (b) the state space dimension is large or both. When the OL is…
Strong stability preserving (SSP) methods are designed primarily for time integration of nonlinear hyperbolic PDEs, for which the permissible SSP step size varies from one step to the next. We develop the first SSP linear multistep methods…
We present a statistical mechanics analysis of the finite-size elasticity of biopolymers, consisting of domains which can exhibit transitions between more than one stable state at large applied force. The constant-force (Gibbs) and…
In high dimensional analysis, effects of explanatory variables on responses sometimes rely on certain exposure variables, such as time or environmental factors. In this paper, to characterize the importance of each predictor, we utilize its…
We show using theory and experiments that a small particle moving along an elastic membrane through a viscous fluid is repelled from the membrane due to hydro-elastic forces. The viscous stress field produces an elastic disturbance leading…
A pinned-free beam in axial fluid flow, subjected to feedback-based actuation at the pinned end, is investigated. The actuation may be a moment or a prescribed angle and it is proportional to the state (curvature, slope, or displacement) of…
Uncertainty principle prohibits the precise measurement of both components of displacement parameters in phase space. We have theoretically shown that this limit can be beaten using single-photon states, in a single-shot and single-mode…
I argue that the limits on this quantity obtained using model-independent parameterizations contain an tacit assumption that could be invalidated under a variety of situations. As a specific example, existing limits on $\Lambda $ would be…
We have analyzed dynamics on the complex free energy landscape of protein folding in the FOLD-X model, by calculating for each state of the system the mean first passage time to the folded state. The resulting kinetic map of the folding…