Related papers: Deconstructing the energy landscape: new algorithm…
The interconversion between left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of…
We present an analytic method, based on the Bohmian equations for quantum mechanics, for approaching the phase-retrieval problem in the following formulation: By knowing the probability density $\left\vert…
Recently, nanofluidics experiments have been used to characterize the behavior of single DNA molecules confined to narrow slits etched with arrays of nanopits. Analysis of the experimental data relies on analytical estimates of the…
In single molecule laser optical tweezer (LOT) pulling experiments a protein or RNA is juxtaposed between DNA handles that are attached to beads in optical traps. The LOT generates folding trajectories under force in terms of time-dependent…
We consider a general model of a heterogeneous polymer chain fluctuating in the proximity of an interface between two selective solvents. The heterogeneous character of the model comes from the fact that the monomer units interact with the…
One of the central problems in epigenetics is how epigenetic modification patterns and chromatin structure are regulated in the cell nucleus. The polymer Potts model, a recently studied model of chromatins, is introduced with an offset in…
An introduction to the application of combinatorial optimization methods to ground state calculations of frustrated, disordered systems is given. We discuss the interface problem in the random bond Ising ferromagnet, the random field Ising…
Nonlinear state-space modelling is a very powerful black-box modelling approach. However powerful, the resulting models tend to be complex, described by a large number of parameters. In many cases interpretability is preferred over…
We establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ensemble of structures that have equal probability of reaching…
We present a mathematically rigorous method for solving three-atomic bound state and scattering problems. The method is well suited for applications in systems where the inter-atomic interaction is of a hard-core nature. It has been…
We have performed chain-growth simulations of minimalistic hybrid lattice models for polymers interacting with interfaces of attractive solid substrates in order to gain insights into the conformational transitions of the polymers in the…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…
Monte Carlo simulations are used to study the conformational properties of a folded semiflexible polymer confined to a long channel. We measure the variation in the conformational free energy with respect to the end-to-end distance of the…
We have developed a theory of polymer entanglement using an extended Cahn-Hilliard functional, with two extra terms. One is a nonlocal attractive term, operating over mesoscales, which is interpreted as giving rise to entanglement, and the…
(abridged) We present a detailed derivation of a simple hydrodynamic two-fluid model, which aims at the description of the phase separation of non-entangled polymer solutions, where viscoelastic effects play a role. It is directly based…
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…
Computing ground states of local Hamiltonians is a fundamental problem in condensed matter physics. We give the first randomized polynomial-time algorithm for finding ground states of gapped one-dimensional Hamiltonians: it outputs an…
The demand for innovative synthetic polymers with improved properties is high, but their structural complexity and vast design space hinder rapid discovery. Machine learning-guided molecular design is a promising approach to accelerate…
In the deformation of layered materials such as geological strata, or stacks of paper, mechanical properties compete with the geometry of layering. Smooth, rounded corners lead to voids between the layers, while close packing of the layers…