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Mechanically induced protein unfolding in the force-clamp apparatus is shown, in a coarse-grained model of ubiquitin, to have lognormal statistics above a treshold force and exponential below it. Correspondingly, the mean unfolding time is…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
In this work, we propose a cascaded scheme of linear Model prediction Control (MPC) based on Control Barrier Functions (CBF) with Dynamic Feedback Linearization (DFL) for Vertical Take-off and Landing (VTOL) Unmanned Aerial Vehicles (UAVs).…
Consistency and reliability are crucial for conducting AI research. Many famous research fields, such as object detection, have been compared and validated with solid benchmark frameworks. After AlphaFold2, the protein folding task has…
We consider the statistical mechanics of a full set of two-dimensional protein-like heteropolymers, whose thermodynamics is characterized by the coil-to-globular ($T_\theta$) and the folding ($T_f$) transition temperatures. For our model,…
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…
In the current AFM experiments the distribution of unfolding times, P(t), is measured by applying a constant stretching force f_s from which the apparent unfolding rate is obtained. To describe the complexity of the underlying energy…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…
We develop a contraction-based framework to establish the existence and exponential stability of periodic solutions in planar nonsmooth dynamical systems governed by Filippov differential inclusions. The method integrates a time- and…
We study the quench dynamics of the three-dimensional Kitaev (spin) model under a linear drive using both exact numerical calculations and analytical "independent crossing approximation". Unlike the two-dimensional Kitaev model, the…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
Centre Manifold analysis of a 3-D nonlinear system with general second order nonlinearities have been worked out. The system is shown to possess two fixed points on the reduced 2-D centre manifold. By introducing a 2-D centre manifold one…
We investigate the linear tearing instability in weakly collisional plasmas using a non-ideal gyrotropic-MHD framework, uncovering a previously unknown scaling relation for the instability growth rate in high-$\beta$ environments. Even…
Kinetically constrained models (KCM) generically have trivial thermodynamics and yet manifest rich glassy dynamics. In order to resolve the thermodynamics-dynamics disconnect in KCMs, we derive a KCM by coarse-graining a non-trivial…
The non-Markovian nature of polymer motions is accounted for in folding kinetics, using frequency-dependent friction. Folding, like many other problems in the physics of disordered systems, involves barrier crossing on a correlated energy…