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The Immersed Boundary Method has long served as a robust computational framework for fluid-structure interactions, yet the rigorous analysis of 1D Peskin filaments anchored to rigid boundaries remains sparse. In this paper, we generalize…
We study the dynamics of bond-disordered Ising spin systems on random graphs with finite connectivity, using generating functional analysis. Rather than disorder-averaged correlation and response functions (as for fully connected systems),…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
We propose a model for motor proteins based on a hierarchical Hamiltonian that we have previously introduced to describe protein folding. The proposed motor model has high efficiency and is consistent with a linear load-velocity response.…
The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…
Equations that govern the temperature-dependence of the rate constants, Gibbs energies,enthalpies, entropies and heat capacities of activation for folding and unfolding of spontaneously-folding fixed two-state systems have been derived…
We investigate one dimensional tight binding model in the presence of a correlated binary disorder. The disorder is due to the interaction of particles with heavy immobile other species. Off-diagonal disorder is created by means of a fast…
Recent years have seen tremendous developments in the use of machine learning models to link amino acid sequence, structure and function of folded proteins. These methods are, however, rarely applicable to the wide range of proteins and…
A mechanical system consisting of an elastic beam under harmonic excitation and an attached sliding body is investigated. Recent experimental observations suggest that the system passively (self-)adapts the axial location of the slider to…
Paper: cond-mat/9311033 The Hubbard model of interacting electrons, like the Ising model of spin-spin interactions, is the simplest possible model displaying many ``real world'' features, but it is much more difficult to analyze…
Motivated by the novel electronic behaviors seen in transition metal oxides, we look for physical insight into disordered, strongly-correlated systems by exploring the atomic limit. In recent work, the atomic limit has provided a useful…
Monte Carlo computer simulations are used to study the conformational free energy of a folded polymer confined to a long cylindrical tube. The polymer is modeled as a hard-sphere chain. Its conformational free energy $F$ is measured as a…
We study the critical Ising model on the square lattice in bounded simply connected domains with + and free boundary conditions. We relate the energy density of the model to a fermionic observable and compute its scaling limit by discrete…
Exactly solvable neural network models with asymmetric weights are rare, and exact solutions are available only in some mean-field approaches. In this article we find exact analytical solutions of an asymmetric spin-glass-like model of…
We consider disordered pinning models, when the return time distribution of the underlying renewal process has a polynomial tail with exponent $\alpha \in (1/2,1)$. This corresponds to a regime where disorder is known to be relevant, i.e.…
We investigate theoretically the effect of polymer tension on the collective behavior of reversibly binding cross-links. For this purpose, we employ a model of two weakly bending wormlike chains aligned in parallel by a tensile force, with…
We report a single-copy tempering method for simulating large complex systems. In a generalized ensemble, the method uses runtime estimate of the thermal average energy computed from a novel integral identity to guide a continuous…
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…
Protein folds are highly designable, in the sense that many sequences fold to the same conformation. In the present work we derive an expression for the designability in a 20 letter lattice model of proteins which, relying only on the…
We introduce a model of proteins in which all of the key atoms in the protein backbone are accounted for, thus extending the Freely Rotating Chain model. We use average bond lengths and average angles from the Protein Databank as input…